WISP-1 is a protein from the CCN protein family which is known to act as an oncogene in most type of cancers to promote cancer cell proliferation, progression, metastasis, and invasion. What might be the structural basis of WISP-1-induced tumor growth?
WNT1 inducible signaling pathway protein 1 (WISP1), a member 4 protein from the CCN family (CCN4), is a secreted matricellular protein found in the extracellular matrix (ECM) and affects different cell responses like other ECM proteins. It plays a part in cellular functions such as differentiation, proliferation, migration, and survival. and was demonstrated to its overexpression has oncogenic properties in most cancers. An in vitro study found that recombinant WISP-1 treatment increased cell proliferation in a breast cancer context (1). Since WISP-1 interacts with other proteins in the ECM to signal downstream pathways, inhibiting the interactions might limit cellular pathway signaling for cellular responses like cell proliferation and halt its oncogenic functions, making it a potential target of cancer therapeutic.
A study on colon cancer found that WISP-1 upregulation is associated with many oncogenic properties of cancerous cells such as proliferation and invasion through increasing apoptosis and blocking cell cycle checkpoints (2). The protein β-catenin was identified as an upstream protein and a direct binding partner of WISP1 in colorectal cancer cells. Together, they mediate the functions of WISP1 through promoting cell proliferation and invasion which initiates colon cancer tumorigenesis. Collectively, these evidence indicates that inhibiting overactive Wnt/β-catenin signaling might be critical in preventing or slowing the pathogenesis of colon cancers (3). Knowing evidence suggests that β-catenin binds WISP-1 to facilitate colon cancer cell proliferation, colony formation, and invasion, inhibiting the interaction between β-catenin and WISP-1 might serve as a therapeutic strategy. The interface of WISP-1 and β-catenin hence warrant further investigation in order to determine competent inhibitors for the interaction. Since no experimental structure of WISP-1 currently exists, generating a model via homology modeling for further interaction analysis (ie moelcular docking) between β-catenin and WISP-1 might provide insights into what consitutes feasible inhibitors in blockage of the interaction.
Sources:
The protein sequence of WISP1 is sourced from the NCBI protein database.
If WISP-1 can bind protein partners to activate signaling pathways like the Wnt/β-catenin signaling pathway to modulate specific cell functions such as tumor cell proliferation, then there are structural domains on WISP-1 that engage in specific interactions with its binding partner β-catenin to promote tumorigenesis in colon cancer.
The protein sequence retrieved from NCBI (Database #1) first undergoes a BLAST search (Method #1) to find potential PDB template for homology modeling
Then the template PDB file (Database #2) will be downloaded and used for homology modeling (Method #2) to construct a 3D model of WISP-1 protein in which no previous experimental structure exists.
The generated model would then be evaluated with an online server PDBsum (Analysis method #1) to gauge its validity for further structural analysis via outputs such as a Ramachandran plot. Then the protein-protein interaction that WISP-1 engaged in would be analyzed with a structure-based online server meta-PPISP (Analysis method #2) to predict protein residues that might be at the interaction interface.
Search CCN family member 4 in NBCI within the protein category, select CCN family member 4 isoform 1 precursor [Homo sapiens]. The protein sequence to be analyzed is NCBI Reference Sequence: NP_003873.1. The search page page should be https://www.ncbi.nlm.nih.gov/protein/NP_003873.1
As a clarificaiton, WISP-1 is CCN4, it is the fourth member of the CCN protein family. (Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462510/)
After getting to the right NCBI site, select “Send to” on the upper right corner, choose FASTA format, and click create file. Upload the “sequence.fasta” file downloaded to the same directory as the Jupyter notebook.
Biopython:
BioPandas
Pandas
Numpy
Modeller
NglView
Prody
!pip install -U ProDy
Requirement already satisfied: ProDy in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (2.2.0)
Requirement already satisfied: pyparsing in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (from ProDy) (3.0.4)
Requirement already satisfied: scipy in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (from ProDy) (1.7.1)
Collecting biopython<=1.76
Using cached biopython-1.76-cp39-cp39-macosx_10_9_x86_64.whl
Requirement already satisfied: numpy>=1.10 in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (from ProDy) (1.20.3)
Installing collected packages: biopython
Attempting uninstall: biopython
Found existing installation: biopython 1.79
Uninstalling biopython-1.79:
Successfully uninstalled biopython-1.79
Successfully installed biopython-1.76
you will need to go to home page --> registration --> sign the License Agreement to obtain a license key from the website and input the license in the correct document file following the error message upon initial attempt of activation. Email containing the license key will arrive within couple of hours when using University of California San Diego for authentification.
conda install modeller
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /Users/yingyinli/opt/anaconda3
added / updated specs:
- modeller
The following packages will be downloaded:
package | build
---------------------------|-----------------
conda-4.13.0 | py39h6e9494a_1 986 KB conda-forge
------------------------------------------------------------
Total: 986 KB
The following packages will be UPDATED:
conda 4.12.0-py39h6e9494a_0 --> 4.13.0-py39h6e9494a_1
Downloading and Extracting Packages
conda-4.13.0 | 986 KB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Note: you may need to restart the kernel to use updated packages.
pip install biopandas
Requirement already satisfied: biopandas in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (0.4.1) Requirement already satisfied: numpy>=1.16.2 in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (from biopandas) (1.20.3) Requirement already satisfied: pandas>=0.24.2 in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (from biopandas) (1.3.4) Requirement already satisfied: setuptools in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (from biopandas) (58.0.4) Requirement already satisfied: python-dateutil>=2.7.3 in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (from pandas>=0.24.2->biopandas) (2.8.2) Requirement already satisfied: pytz>=2017.3 in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (from pandas>=0.24.2->biopandas) (2021.3) Requirement already satisfied: six>=1.5 in /Users/yingyinli/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.7.3->pandas>=0.24.2->biopandas) (1.16.0) Note: you may need to restart the kernel to use updated packages.
from Bio import SeqIO
import numpy as np
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
from biopandas.pdb import PandasPdb
import pandas as pd
import Bio
from Bio.PDB import PDBList
from prody import *
from modeller.automodel import *
from modeller import soap_protein_od
import pickle
from modeller import *
from Bio.PDB import *
import nglview as ngv
env = environ()
environ____W> The class 'environ' is deprecated; use 'Environ' instead
Performing Bioinformatics Analysis (20 points)
#read in the fasta file downloaded from NCBI
#WISP1_protein is a global variable
WISP1_protein = SeqIO.read('sequence.fasta', 'fasta')
#code check
print(WISP1_protein)
ID: NP_003873.1
Name: NP_003873.1
Description: NP_003873.1 CCN family member 4 isoform 1 precursor [Homo sapiens]
Number of features: 0
Seq('MRWFLPWTLAAVTAAAASTVLATALSPAPTTMDFTPAPLEDTSSRPQFCKWPCE...IAN', SingleLetterAlphabet())
5 points for use of a built-in Bioconductor or Biopython function (or some other tool that was discussed in class like NumPy or SciPy), and description of what the function reads in and what it returns.
The Biopython function used: Bio.SeqIO.read()
What the function reads in: a handle containing only 1 record and format
What the function returns: the content in the sequence fasta file read in
#extract the string for using blastpdb function to cross check if potential blast template has an existing pdb structure on file
#the blastPDB function within the Prody module require a string input as protein sequence
#WISP1_protein_seq is a global variable
WISP1_protein_seq = WISP1_protein.seq
#code check
str(WISP1_protein_seq)
'MRWFLPWTLAAVTAAAASTVLATALSPAPTTMDFTPAPLEDTSSRPQFCKWPCECPPSPPRCPLGVSLITDGCECCKMCAQQLGDNCTEAAICDPHRGLYCDYSGDRPRYAIGVCAQVVGVGCVLDGVRYNNGQSFQPNCKYNCTCIDGAVGCTPLCLRVRPPRLWCPHPRRVSIPGHCCEQWVCEDDAKRPRKTAPRDTGAFDAVGEVEAWHRNCIAYTSPWSPCSTSCGLGVSTRISNVNAQCWPEQESRLCNLRPCDVDIHTLIKAGKKCLAVYQPEASMNFTLAGCISTRSYQPKYCGVCMDNRCCIPYKSKTIDVSFQCPDGLGFSRQVLWINACFCNLSCRNPNDIFADLESYPDFSEIAN'
Blast code source: http://prody.csb.pitt.edu/tutorials/structure_analysis/blastpdb.html
#BLAST search with blastPDB() function from Prody, taking in protein sequence in string as an input
#blastPDB() is a function that can check if structures matching a sequence exist in PDB, which will be the template file in PDB which we would use fo homology modeling
blast_record = blastPDB(str(WISP1_protein_seq))
@> Blast searching NCBI PDB database for "MRWFL..." @> Blast search completed in 8.3s.
#save this BLAST record on disk, as NCBI may not respond to repeated searches for the same sequence
pickle.dump(blast_record, open('WISP1_blast_record.pkl', 'wb'))
blast_record = pickle.load(open('WISP1_blast_record.pkl', 'rb'))
#blast_record is a global variable
#5 points for a function written that performs some part of the bioinformatics analyses
#write a function for template selection and display relevant evaluation data for the chosen template
def select_best ():
#best is a local variable and scope is limited to the function only
best = blast_record.getBest()
print ('The PDB ID for the best template is ' + str (best['pdb_id']))
print ('Its percent identity is ' + str(best['percent_identity']))
print ('Its e-value is ' + str(best['evalue']))
#use the function to select the most suitable template for homology modeling
select_best ()
The PDB ID for the best template is 5nb8 Its percent identity is 53.521126760563384 Its e-value is 2.45677e-19
Code Source: https://salilab.org/modeller/tutorial/basic.html
#import 5nb8 PDB structure & put in the same directory as notebook
pdbl=PDBList()
pdbl.retrieve_pdb_file('5nb8',file_format='pdb',pdir='/Users/yingyinli//BIMM143/6-5 Project 2D')
Downloading PDB structure '5nb8'...
'/Users/yingyinli//BIMM143/6-5 Project 2D/pdb5nb8.ent'
#rename downloaded pdb to run the next function that takes in argument in specific naming format
!mv pdb5nb8.ent 5nb8.pdb
For the alignment step performed below, you would need to manually create the document 'WISP1.ali' on an empty txt file in the same directory as the notebook (have been cleared by the professor to do so as modeller document did not contain information of how to generate the file).
what should go in the file:
The rest of the file contains the sequence of WISP1, with "*" marking its end. The standard one-letter amino acid codes are used.
for details and a sample document format, refers to documentation of Modeller https://salilab.org/modeller/tutorial/basic.html
#aligning WISP1 with the template 5nb8 with the align2d() command in MODELLER
#The following MODELLER script aligns the WISP-1 sequence in file "WISP1.ali" with the 1bdm:A structure in the PDB file "1bdm.pdb"
from modeller import *
#create an 'Environ' object to use as input to later commands
env = Environ()
#create an empty alignment 'aln'
aln = Alignment(env)
#create a new protein model 'mdl' which read the chain A segment of the 5nb8 PDB structure file
mdl = Model(env, file='5nb8', model_segment=('FIRST:A','LAST:A'))
#The append_model() command transfers the PDB sequence of the 5nb8 model to the alignment and assigns it the name of "5nb8" (align_codes)
aln.append_model(mdl, align_codes='5nb8', atom_files='5nb8.pdb')
#add the "WISP-1" sequence from file "WISP1.ali" to the alignment, using the append() command
aln.append(file='WISP1.ali', align_codes='WISP1')
#The align2d() command is executed to align the two sequences
aln.align2d(max_gap_length=50)
aln.write(file='WISP1-5nb8.ali', alignment_format='PIR') #PAP easier to visualize
aln.write(file='WISP1-5nb8.pap', alignment_format='PAP') #PIR is what modeller works with
mkapsa__637W> No residue topology library is in memory.
Better radii would be used if topology.read() is called first.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: N --> N
This message is written only for the first such atom.
Pairwise dynamic programming alignment (ALIGN2D):
Residue-residue metric : $(LIB)/as1.sim.mat
Diagonal : 100
Overhang : 0
Maximal gap length : 50
Local alignment : F
MATRIX_OFFSET (local aln): 0.0000
FIX_OFFSETS : 0.0 -1.0 -2.0 -3.0 -4.0
N_SUBOPT : 0
SUBOPT_OFFSET : 0.0000
Alignment block : 1
Gap introduction penalty : -100.0000
Gap extension penalty : 0.0000
Gap diagonal penalty : 0.0000
Structure gap penalties : 3.500 3.500 3.500 0.200 4.000 6.500 2.000 0.000
Break-break bonus : 10000.0000
Length of alignment : 367
Score : 48435.6133
#Observe the alignment of the template 5nb8 and the target WISP1.
!cat WISP1-5nb8.pap
_aln.pos 10 20 30 40 50 60 5nb8 M--------------------------------------E---------------------------- WISP1 MRWFLPWTLAAVTAAAASTVLATALSPAPTTMDFTPAPLEDTSSRPQFCKWPCECPPSPPRCPLGVSL _consrvd * * _aln.p 70 80 90 100 110 120 130 5nb8 ---------------GDNC------------------------------------VFDGVIYRNGEKF WISP1 ITDGCECCKMCAQQLGDNCTEAAICDPHRGLYCDYSGDRPRYAIGVCAQVVGVGCVLDGVRYNNGQSF _consrvd **** * *** * ** * _aln.pos 140 150 160 170 180 190 200 5nb8 EPNCQYHCTCRDGQIGCVPRCQ------L------DVLLPG--------------P------D----- WISP1 QPNCKYNCTCIDGAVGCTPLCLRVRPPRLWCPHPRRVSIPGHCCEQWVCEDDAKRPRKTAPRDTGAFD _consrvd *** * *** ** ** * * * * ** * * _aln.pos 210 220 230 240 250 260 270 5nb8 ---------------------C-----------------------------------------PAPKK WISP1 AVGEVEAWHRNCIAYTSPWSPCSTSCGLGVSTRISNVNAQCWPEQESRLCNLRPCDVDIHTLIKAGKK _consrvd * * ** _aln.pos 280 290 300 310 320 330 340 5nb8 -VAV--P---------G------------------ECC---------EKWTCG--------------- WISP1 CLAVYQPEASMNFTLAGCISTRSYQPKYCGVCMDNRCCIPYKSKTIDVSFQCPDGLGFSRQVLWINAC _consrvd ** * * ** * _aln.pos 350 360 5nb8 --------------------------- WISP1 FCNLSCRNPNDIFADLESYPDFSEIAN _consrvd
#from the target-template alignment, Modeller uses its AutoModel class to construct a 3D model of the target automatically
env = Environ()
#create an AutoModel object, call it 'a', and set parameters to guide the model building procedure
#assess_methods requests assessment scores on the models generated
#a is a global variable
a = AutoModel(env, alnfile='WISP1-5nb8.ali',
knowns='5nb8', sequence='WISP1',
assess_methods=(assess.DOPE,
soap_protein_od.Scorer(),
assess.GA341))
#starting_model and ending_model define the number of models that are calculated
a.starting_model = 1
a.ending_model = 5
#the make method actually calculates the models
a.make()
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
----------------------------------------------
END OF TABLE
read_to_681_> topology.submodel read from topology file: 3
patch_s_522_> Number of disulfides patched in MODEL: 5
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 16583 13904
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: ASN:OXT ASN
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 350313
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -19561.4375
<< end of ENERGY.
DOPE score : -19561.437500
>> Model assessment by SOAP-Protein-OD score
preppdf_455W> None of the non-bonded terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3918541
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 999.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 0.0000
<< end of ENERGY.
SOAP-Protein-OD score : 0.000000
>> Model assessment by GA341 potential
Surface library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/surf5.de
Pair library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 62.856998
Sequence length : 367
Compactness : 0.012427
Native energy (pair) : 74.187079
Native energy (surface) : 41.164093
Native energy (combined) : 8.783159
Z score (pair) : -3.828903
Z score (surface) : -1.095584
Z score (combined) : -3.287000
GA341 score : 0.973716
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4418
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 2115.5510
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 2881 0 0 0.003 0.003 8.0481 1.000
2 Bond angle potential : 3935 0 1 1.786 1.786 236.08 1.000
3 Stereochemical cosine torsion poten: 1962 0 81 50.259 50.259 768.76 1.000
4 Stereochemical improper torsion pot: 1155 0 0 0.938 0.938 21.032 1.000
5 Soft-sphere overlap restraints : 4418 0 0 0.003 0.003 3.5749 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 765 0 4 1.295 1.295 108.48 1.000
10 Distance restraints 2 (N-O) : 973 0 11 1.669 1.669 178.00 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 366 0 0 3.338 3.338 48.102 1.000
14 Sidechain Chi_1 dihedral restraints: 315 0 2 84.674 84.674 97.588 1.000
15 Sidechain Chi_2 dihedral restraints: 209 0 1 76.192 76.192 86.232 1.000
16 Sidechain Chi_3 dihedral restraints: 98 0 0 80.861 80.861 52.483 1.000
17 Sidechain Chi_4 dihedral restraints: 34 0 0 105.462 105.462 23.723 1.000
18 Disulfide distance restraints : 5 0 0 0.007 0.007 0.39089E-01 1.000
19 Disulfide angle restraints : 10 0 0 1.873 1.873 0.77495 1.000
20 Disulfide dihedral angle restraints: 5 0 0 20.174 20.174 2.0034 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 643 0 0 0.630 0.630 31.940 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 365 205 54 37.936 134.248 416.39 1.000
26 Distance restraints 4 (SDCH-SDCH) : 183 0 2 2.228 2.228 32.307 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: WISP1.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 61820.8125
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 9954 1M 2R C N 7 9 -142.52 -125.20 17.41 0.65 -63.00 -166.38 31.59
1 2R 2R N CA 9 10 142.36 140.60 -41.10
2 9955 2R 3W C N 18 20 -119.80 -124.90 15.85 0.64 -63.00 -178.30 20.20
2 3W 3W N CA 20 21 128.39 143.40 -44.20
3 9956 3W 4F C N 32 34 -111.47 -124.20 34.32 1.25 -63.20 163.04 19.70
3 4F 4F N CA 34 35 111.43 143.30 -44.30
4 9957 4F 5L C N 43 45 -132.67 -108.50 29.60 1.63 -63.50 171.21 21.05
4 5L 5L N CA 45 46 115.41 132.50 -41.20
5 9959 6P 7W C N 58 60 -165.89 -124.90 47.36 1.55 -63.00 -179.19 29.48
5 7W 7W N CA 60 61 167.12 143.40 -44.20
6 9960 7W 8T C N 72 74 -117.76 -124.80 10.73 0.64 -63.20 175.03 26.07
6 8T 8T N CA 74 75 151.59 143.50 -42.10
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42 65G 65G N CA 483 484 173.59 174.60 8.50
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46 71D 71D N CA 523 524 32.91 114.20 -40.00
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47 72G 72G N CA 531 532 -179.18 -166.10 8.50
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59 93C 93C N CA 676 677 -53.43 -41.10 141.10
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64 100Y 100Y N CA 730 731 131.14 128.40 -43.40
65 10054 101C 102D C N 746 748 -94.63 -96.50 2.07 0.08 -63.30 158.22 17.86
65 102D 102D N CA 748 749 115.09 114.20 -40.00
66 10055 102D 103Y C N 754 756 -133.05 -124.30 25.72 1.05 -63.50 171.72 30.69
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67 10056 103Y 104S C N 766 768 -72.91 -72.40 18.24 1.06 -64.10 154.62 11.75
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68 106D 106D N CA 778 779 158.89 150.30 -40.00
69 10059 106D 107R C N 784 786 -69.54 -72.10 3.68 0.24 -63.00 179.76 24.72
69 107R 107R N CA 786 787 139.26 141.90 -41.10
70 10061 108P 109R C N 802 804 -89.93 -72.10 25.60 1.66 -63.00 160.90 23.59
70 109R 109R N CA 804 805 160.27 141.90 -41.10
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71 110Y 110Y N CA 815 816 130.40 128.40 -43.40
72 10063 110Y 111A C N 825 827 -110.95 -134.00 27.60 0.67 -62.50 179.38 27.46
72 111A 111A N CA 827 828 131.81 147.00 -40.90
73 10065 112I 113G C N 838 840 -67.71 -80.20 53.97 1.54 82.20 -172.21 6.94
73 113G 113G N CA 840 841 121.60 174.10 8.50
74 10067 114V 115C C N 849 851 -58.21 -63.00 13.35 1.39 -117.90 175.79 7.63
74 115C 115C N CA 851 852 -53.56 -41.10 141.10
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75 116A 116A N CA 857 858 137.70 147.00 -40.90
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77 120G 120G N CA 885 886 -150.29 174.10 8.50
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78 126D 126D N CA 921 922 -160.92 150.30 40.90
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79 127G 127G N CA 929 930 -36.98 -41.20 8.50
80 10111 158L 159R C N 1163 1165 -145.23 -125.20 30.36 0.95 -63.00 175.89 29.33
80 159R 159R N CA 1165 1166 163.41 140.60 -41.10
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82 166W 166W N CA 1227 1228 102.76 139.00 -44.20
83 10122 169H 170P C N 1262 1264 -70.41 -58.70 25.28 1.48 -64.50 155.40 11.91
83 170P 170P N CA 1264 1265 -8.09 -30.50 147.20
84 10123 170P 171R C N 1269 1271 -70.21 -72.10 50.32 3.91 -63.00 126.92 17.63
84 171R 171R N CA 1271 1272 -167.82 141.90 -41.10
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85 178H 178H N CA 1325 1326 166.36 138.80 -42.30
86 10133 180C 181E C N 1345 1347 -70.97 -69.30 14.15 1.02 -63.60 163.31 22.18
86 181E 181E N CA 1347 1348 156.56 142.50 -40.30
87 10134 181E 182Q C N 1354 1356 -61.48 -73.00 18.62 1.07 -63.80 166.39 24.59
87 182Q 182Q N CA 1356 1357 126.07 140.70 -40.30
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88 183W 183W N CA 1365 1366 -173.56 143.40 -44.20
89 10138 185C 186E C N 1390 1392 -78.24 -69.30 19.40 1.17 -63.60 160.65 22.23
89 186E 186E N CA 1392 1393 159.72 142.50 -40.30
90 10140 187D 188D C N 1407 1409 -122.47 -96.50 26.00 1.06 -63.30 166.15 17.85
90 188D 188D N CA 1409 1410 115.26 114.20 -40.00
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91 189A 189A N CA 1417 1418 142.39 147.00 -40.90
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92 190K 190K N CA 1422 1423 127.77 139.10 -40.80
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93 191R 191R N CA 1431 1432 119.56 140.60 -41.10
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94 193R 193R N CA 1449 1450 149.77 141.90 -41.10
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95 194K 194K N CA 1460 1461 121.88 140.40 -40.80
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97 197P 197P N CA 1481 1482 -19.80 -30.50 147.20
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98 198R 198R N CA 1488 1489 139.42 140.60 -41.10
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99 200T 200T N CA 1507 1508 153.18 143.50 -42.10
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100 201G 201G N CA 1514 1515 175.61 174.60 8.50
101 10154 201G 202A C N 1516 1518 -164.33 -134.00 43.76 1.35 -62.50 173.57 33.81
101 202A 202A N CA 1518 1519 178.54 147.00 -40.90
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102 203F 203F N CA 1523 1524 119.38 140.70 -44.30
103 10156 203F 204D C N 1532 1534 -120.33 -96.50 43.66 1.84 -63.30 178.57 25.73
103 204D 204D N CA 1534 1535 150.78 114.20 -40.00
104 10157 204D 205A C N 1540 1542 -123.05 -134.00 13.43 0.74 -62.50 175.13 31.94
104 205A 205A N CA 1542 1543 154.78 147.00 -40.90
105 10159 206V 207G C N 1552 1554 -123.29 -80.20 43.67 2.67 82.20 -128.29 17.57
105 207G 207G N CA 1554 1555 -178.82 174.10 8.50
106 10160 207G 208E C N 1556 1558 -68.85 -69.30 1.14 0.10 -63.60 176.23 23.79
106 208E 208E N CA 1558 1559 143.55 142.50 -40.30
107 10162 209V 210E C N 1572 1574 -127.13 -63.60 96.56 16.20 -63.60 96.56 16.20
107 210E 210E N CA 1574 1575 -113.02 -40.30 -40.30
108 10163 210E 211A C N 1581 1583 -58.06 -68.20 10.37 0.95 -62.50 171.67 27.92
108 211A 211A N CA 1583 1584 147.49 145.30 -40.90
109 10164 211A 212W C N 1586 1588 -65.87 -71.30 26.58 1.86 -63.00 157.21 19.48
109 212W 212W N CA 1588 1589 112.98 139.00 -44.20
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110 213H 213H N CA 1602 1603 159.00 138.80 -42.30
111 10166 213H 214R C N 1610 1612 -158.17 -125.20 49.58 1.55 -63.00 170.34 29.31
111 214R 214R N CA 1612 1613 177.63 140.60 -41.10
112 10168 215N 216C C N 1629 1631 -65.90 -63.00 7.86 1.18 -117.90 178.24 7.66
112 216C 216C N CA 1631 1632 -48.40 -41.10 141.10
113 10170 217I 218A C N 1643 1645 -78.60 -68.20 46.92 3.42 -62.50 129.05 21.98
113 218A 218A N CA 1645 1646 -168.94 145.30 -40.90
114 10171 218A 219Y C N 1648 1650 -27.18 -98.40 72.87 3.03 -63.50 176.55 26.25
114 219Y 219Y N CA 1650 1651 143.82 128.40 -43.40
115 10172 219Y 220T C N 1660 1662 -54.36 -78.10 24.85 1.30 -63.20 175.64 21.95
115 220T 220T N CA 1662 1663 142.48 149.80 -42.10
116 10173 220T 221S C N 1667 1669 -162.43 -136.60 44.48 1.58 -64.10 169.11 19.35
116 221S 221S N CA 1669 1670 -172.59 151.20 -35.00
117 10175 222P 223W C N 1680 1682 -109.22 -124.90 17.13 0.59 -63.00 -174.83 26.20
117 223W 223W N CA 1682 1683 136.49 143.40 -44.20
118 10176 223W 224S C N 1694 1696 -147.48 -136.60 18.77 1.06 -64.10 -169.84 12.06
118 224S 224S N CA 1696 1697 135.90 151.20 -35.00
119 10180 227S 228T C N 1719 1721 -149.00 -124.80 26.39 1.09 -63.20 -175.03 29.27
119 228T 228T N CA 1721 1722 154.03 143.50 -42.10
120 10181 228T 229S C N 1726 1728 -139.94 -136.60 3.92 0.21 -64.10 -168.50 19.27
120 229S 229S N CA 1728 1729 149.16 151.20 -35.00
121 10183 230C 231G C N 1738 1740 -146.86 -167.20 23.33 0.38 82.20 -157.35 15.26
121 231G 231G N CA 1740 1741 163.17 174.60 8.50
122 10184 231G 232L C N 1742 1744 -114.02 -108.50 8.16 0.46 -63.50 175.14 21.99
122 232L 232L N CA 1744 1745 126.49 132.50 -41.20
123 10185 232L 233G C N 1750 1752 133.87 -167.20 58.95 1.16 82.20 172.29 10.83
123 233G 233G N CA 1752 1753 172.86 174.60 8.50
124 10187 234V 235S C N 1761 1763 -164.99 -136.60 28.49 1.07 -64.10 -161.05 21.68
124 235S 235S N CA 1763 1764 153.53 151.20 -35.00
125 10188 235S 236T C N 1767 1769 -121.47 -124.80 36.02 1.45 -63.20 160.68 17.48
125 236T 236T N CA 1769 1770 107.64 143.50 -42.10
126 10189 236T 237R C N 1774 1776 -134.58 -125.20 9.41 0.36 -63.00 -168.62 30.77
126 237R 237R N CA 1776 1777 141.41 140.60 -41.10
127 10191 238I 239S C N 1793 1795 -109.30 -136.60 50.82 1.87 -64.10 150.29 9.26
127 239S 239S N CA 1795 1796 108.33 151.20 -35.00
128 10192 239S 240N C N 1799 1801 -119.65 -119.90 2.85 0.12 -63.20 -175.87 20.45
128 240N 240N N CA 1801 1802 134.17 137.00 -41.10
129 10194 241V 242N C N 1814 1816 -71.44 -71.20 6.96 0.44 -63.20 169.35 21.63
129 242N 242N N CA 1816 1817 149.76 142.80 -41.10
130 10195 242N 243A C N 1822 1824 -63.93 -68.20 30.54 2.31 -62.50 155.96 25.49
130 243A 243A N CA 1824 1825 115.06 145.30 -40.90
131 10196 243A 244Q C N 1827 1829 -175.80 -121.10 74.39 2.38 -63.80 171.28 30.57
131 244Q 244Q N CA 1829 1830 -169.89 139.70 -40.30
132 10197 244Q 245C C N 1836 1838 -58.54 -63.00 20.48 2.24 -117.90 168.60 7.34
132 245C 245C N CA 1838 1839 -61.09 -41.10 141.10
133 10198 245C 246W C N 1842 1844 -167.47 -124.90 43.04 2.05 -63.00 -152.94 32.91
133 246W 246W N CA 1844 1845 137.02 143.40 -44.20
134 10200 247P 248E C N 1863 1865 -81.88 -69.30 16.42 1.51 -63.60 173.21 22.14
134 248E 248E N CA 1865 1866 131.94 142.50 -40.30
135 10201 248E 249Q C N 1872 1874 -85.88 -73.00 13.93 0.89 -63.80 175.10 26.92
135 249Q 249Q N CA 1874 1875 146.00 140.70 -40.30
136 10202 249Q 250E C N 1881 1883 -119.63 -117.80 14.64 0.76 -63.60 171.96 20.42
136 250E 250E N CA 1883 1884 122.28 136.80 -40.30
137 10203 250E 251S C N 1890 1892 63.13 -72.40 135.62 9.83 -64.10 -149.64 15.19
137 251S 251S N CA 1892 1893 157.47 152.40 -35.00
138 10204 251S 252R C N 1896 1898 -111.77 -125.20 83.32 3.71 -63.00 110.78 12.61
138 252R 252R N CA 1898 1899 58.37 140.60 -41.10
139 10205 252R 253L C N 1907 1909 -135.79 -108.50 32.41 1.77 -63.50 172.13 21.13
139 253L 253L N CA 1909 1910 115.02 132.50 -41.20
140 10207 254C 255N C N 1921 1923 -100.34 -119.90 22.08 1.14 -63.20 175.64 24.07
140 255N 255N N CA 1923 1924 147.24 137.00 -41.10
141 10209 256L 257R C N 1937 1939 138.70 -125.20 98.95 3.39 -63.00 -138.67 39.69
141 257R 257R N CA 1939 1940 164.21 140.60 -41.10
142 10211 258P 259C C N 1955 1957 -66.93 -63.00 4.42 0.79 -117.90 -176.99 7.84
142 259C 259C N CA 1957 1958 -43.13 -41.10 141.10
143 10212 259C 260D C N 1961 1963 -67.92 -70.90 5.36 0.18 -63.30 174.22 21.79
143 260D 260D N CA 1963 1964 145.85 150.30 -40.00
144 10214 261V 262D C N 1976 1978 -96.42 -70.90 46.96 1.60 -63.30 134.42 18.72
144 262D 262D N CA 1978 1979 -170.28 150.30 -40.00
145 10216 263I 264H C N 1992 1994 59.75 56.30 5.95 0.48 -63.20 145.73 25.01
145 264H 264H N CA 1994 1995 35.95 40.80 -42.30
146 10217 264H 265T C N 2002 2004 -107.87 -124.80 16.96 0.92 -63.20 178.99 25.93
146 265T 265T N CA 2004 2005 144.58 143.50 -42.10
147 10218 265T 266L C N 2009 2011 -105.71 -108.50 17.11 0.95 -63.50 174.59 26.83
147 266L 266L N CA 2011 2012 149.38 132.50 -41.20
148 10222 269A 270G C N 2039 2041 137.89 78.70 67.56 3.79 -80.20 151.26 8.02
148 270G 270G N CA 2041 2042 -133.53 -166.10 174.10
149 10229 276V 277Y C N 2087 2089 168.78 -124.30 66.99 5.13 -63.50 -142.73 29.97
149 277Y 277Y N CA 2089 2090 132.36 135.40 -43.40
150 10230 277Y 278Q C N 2099 2101 -72.74 -73.00 9.47 0.61 -63.80 171.77 24.80
150 278Q 278Q N CA 2101 2102 131.24 140.70 -40.30
151 10232 279P 280E C N 2115 2117 -99.49 -117.80 25.55 1.36 -63.60 168.94 24.55
151 280E 280E N CA 2117 2118 154.62 136.80 -40.30
152 10233 280E 281A C N 2124 2126 -62.10 -68.20 10.32 0.65 -62.50 177.88 29.17
152 281A 281A N CA 2126 2127 136.98 145.30 -40.90
153 10234 281A 282S C N 2129 2131 -126.81 -136.60 23.76 0.96 -64.10 176.10 10.87
153 282S 282S N CA 2131 2132 129.55 151.20 -35.00
154 10236 283M 284N C N 2143 2145 -76.27 -71.20 9.93 0.77 -63.20 175.85 21.29
154 284N 284N N CA 2145 2146 134.26 142.80 -41.10
155 10239 286T 287L C N 2169 2171 -108.56 -108.50 7.55 0.41 -63.50 -175.66 28.36
155 287L 287L N CA 2171 2172 140.05 132.50 -41.20
156 10240 287L 288A C N 2177 2179 -121.06 -134.00 14.53 0.33 -62.50 -171.93 33.94
156 288A 288A N CA 2179 2180 140.38 147.00 -40.90
157 10244 291I 292S C N 2200 2202 -76.90 -72.40 8.13 0.37 -64.10 166.33 12.86
157 292S 292S N CA 2202 2203 159.16 152.40 -35.00
158 10245 292S 293T C N 2206 2208 -130.19 -124.80 27.91 1.04 -63.20 161.56 25.10
158 293T 293T N CA 2208 2209 170.88 143.50 -42.10
159 10246 293T 294R C N 2213 2215 -109.76 -125.20 18.58 0.55 -63.00 177.63 21.26
159 294R 294R N CA 2215 2216 130.27 140.60 -41.10
160 10247 294R 295S C N 2224 2226 -145.36 -136.60 14.47 0.82 -64.10 -167.34 12.12
160 295S 295S N CA 2226 2227 139.68 151.20 -35.00
161 10248 295S 296Y C N 2230 2232 -121.01 -124.30 13.24 0.57 -63.50 175.66 25.24
161 296Y 296Y N CA 2232 2233 122.57 135.40 -43.40
162 10249 296Y 297Q C N 2242 2244 -146.68 -121.10 32.18 1.00 -63.80 -179.38 30.86
162 297Q 297Q N CA 2244 2245 159.22 139.70 -40.30
163 10251 298P 299K C N 2258 2260 73.10 56.60 128.53 10.46 -62.90 -155.19 24.44
163 299K 299K N CA 2260 2261 166.07 38.60 -40.80
164 10252 299K 300Y C N 2267 2269 -105.47 -98.40 13.58 1.23 -63.50 165.62 24.28
164 300Y 300Y N CA 2269 2270 116.81 128.40 -43.40
165 10254 301C 302G C N 2285 2287 -155.42 -167.20 17.05 0.39 82.20 -163.48 14.68
165 302G 302G N CA 2287 2288 162.28 174.60 8.50
166 10257 304C 305M C N 2302 2304 -73.63 -73.00 41.78 2.81 -63.40 135.11 20.98
166 305M 305M N CA 2304 2305 -175.22 143.00 -40.50
167 10258 305M 306D C N 2310 2312 -76.42 -96.50 61.47 2.59 -63.30 97.00 11.24
167 306D 306D N CA 2312 2313 56.11 114.20 -40.00
168 10259 306D 307N C N 2318 2320 -117.88 -119.90 4.82 0.26 -63.20 -174.25 26.34
168 307N 307N N CA 2320 2321 141.38 137.00 -41.10
169 10264 311I 312P C N 2357 2359 -59.09 -58.70 2.24 0.22 -64.50 179.99 13.15
169 312P 312P N CA 2359 2360 -32.71 -30.50 147.20
170 10266 313Y 314K C N 2376 2378 -74.82 -70.20 8.35 0.51 -62.90 172.26 23.04
170 314K 314K N CA 2378 2379 147.35 140.40 -40.80
171 10268 315S 316K C N 2391 2393 -80.99 -70.20 11.68 0.94 -62.90 177.66 22.14
171 316K 316K N CA 2393 2394 135.93 140.40 -40.80
172 10269 316K 317T C N 2400 2402 -125.08 -124.80 31.59 1.36 -63.20 165.98 18.00
172 317T 317T N CA 2402 2403 111.91 143.50 -42.10
173 10270 317T 318I C N 2407 2409 -68.01 -63.40 5.41 1.02 -120.60 -175.61 8.60
173 318I 318I N CA 2409 2410 -46.43 -43.60 130.30
174 10271 318I 319D C N 2415 2417 160.90 -96.50 119.88 4.98 -63.30 -162.21 32.71
174 319D 319D N CA 2417 2418 176.20 114.20 -40.00
175 10272 319D 320V C N 2423 2425 -61.42 -62.40 8.47 1.02 -73.50 170.41 14.71
175 320V 320V N CA 2425 2426 -50.81 -42.40 139.20
176 10278 325P 326D C N 2469 2471 -169.04 -70.90 130.12 5.64 -63.30 135.21 22.86
176 326D 326D N CA 2471 2472 -124.27 150.30 -40.00
177 10280 327G 328L C N 2481 2483 -61.72 -70.70 20.39 1.28 -63.50 164.51 22.94
177 328L 328L N CA 2483 2484 123.30 141.60 -41.20
178 10282 329G 330F C N 2493 2495 -139.95 -124.20 18.92 0.49 -63.20 179.19 29.84
178 330F 330F N CA 2495 2496 153.78 143.30 -44.30
179 10283 330F 331S C N 2504 2506 -111.05 -136.60 25.64 0.96 -64.10 -177.83 16.43
179 331S 331S N CA 2506 2507 148.98 151.20 -35.00
180 10284 331S 332R C N 2510 2512 -73.20 -72.10 1.11 0.09 -63.00 177.42 24.66
180 332R 332R N CA 2512 2513 141.77 141.90 -41.10
181 10285 332R 333Q C N 2521 2523 -124.63 -121.10 17.96 0.79 -63.80 173.41 28.72
181 333Q 333Q N CA 2523 2524 157.31 139.70 -40.30
182 10287 334V 335L C N 2537 2539 -109.13 -108.50 2.25 0.11 -63.50 -178.31 23.04
182 335L 335L N CA 2539 2540 134.67 132.50 -41.20
183 10288 335L 336W C N 2545 2547 -142.02 -124.90 22.05 0.70 -63.00 177.11 27.46
183 336W 336W N CA 2547 2548 157.29 143.40 -44.20
184 10290 337I 338N C N 2567 2569 -121.33 -119.90 7.56 0.37 -63.20 -179.70 19.94
184 338N 338N N CA 2569 2570 129.57 137.00 -41.10
185 10291 338N 339A C N 2575 2577 -145.27 -134.00 11.63 0.29 -62.50 -171.61 35.31
185 339A 339A N CA 2577 2578 149.87 147.00 -40.90
186 10293 340C 341F C N 2586 2588 -137.35 -124.20 13.41 0.60 -63.20 -169.93 31.23
186 341F 341F N CA 2588 2589 140.69 143.30 -44.30
187 10295 342C 343N C N 2603 2605 -138.03 -119.90 19.48 0.63 -63.20 -169.85 28.01
187 343N 343N N CA 2605 2606 144.10 137.00 -41.10
188 10296 343N 344L C N 2611 2613 -125.03 -108.50 18.58 0.99 -63.50 176.31 21.85
188 344L 344L N CA 2613 2614 124.03 132.50 -41.20
189 10297 344L 345S C N 2619 2621 -132.88 -136.60 10.32 0.43 -64.10 -170.50 11.71
189 345S 345S N CA 2621 2622 141.58 151.20 -35.00
190 10299 346C 347R C N 2631 2633 -138.62 -125.20 16.11 0.48 -63.00 -174.50 30.23
190 347R 347R N CA 2633 2634 149.51 140.60 -41.10
191 10300 347R 348N C N 2642 2644 -111.97 -119.90 14.69 0.47 -63.20 172.76 19.33
191 348N 348N N CA 2644 2645 124.64 137.00 -41.10
192 10302 349P 350N C N 2657 2659 -116.73 -119.90 21.37 0.89 -63.20 165.84 18.34
192 350N 350N N CA 2659 2660 115.87 137.00 -41.10
193 10303 350N 351D C N 2665 2667 -134.81 -96.50 38.37 1.56 -63.30 168.21 17.88
193 351D 351D N CA 2667 2668 112.25 114.20 -40.00
194 10305 352I 353F C N 2681 2683 -113.65 -124.20 24.95 0.87 -63.20 172.54 20.88
194 353F 353F N CA 2683 2684 120.69 143.30 -44.30
195 10306 353F 354A C N 2692 2694 -169.18 -134.00 36.73 0.89 -62.50 -166.39 37.38
195 354A 354A N CA 2694 2695 157.54 147.00 -40.90
196 10307 354A 355D C N 2697 2699 -124.81 -96.50 43.61 1.79 -63.30 135.76 14.41
196 355D 355D N CA 2699 2700 81.03 114.20 -40.00
197 10308 355D 356L C N 2705 2707 -111.58 -108.50 5.86 0.33 -63.50 175.43 22.11
197 356L 356L N CA 2707 2708 127.51 132.50 -41.20
198 10309 356L 357E C N 2713 2715 -109.27 -117.80 11.51 0.36 -63.60 175.42 21.22
198 357E 357E N CA 2715 2716 129.07 136.80 -40.30
199 10310 357E 358S C N 2722 2724 -75.74 -72.40 5.48 0.43 -64.10 177.33 13.57
199 358S 358S N CA 2724 2725 148.05 152.40 -35.00
200 10311 358S 359Y C N 2728 2730 -120.00 -124.30 11.12 0.45 -63.50 177.76 25.60
200 359Y 359Y N CA 2730 2731 125.14 135.40 -43.40
201 10313 360P 361D C N 2747 2749 -104.13 -96.50 22.81 0.95 -63.30 138.84 15.15
201 361D 361D N CA 2749 2750 92.71 114.20 -40.00
202 10314 361D 362F C N 2755 2757 -126.98 -124.20 3.14 0.08 -63.20 -177.55 29.54
202 362F 362F N CA 2757 2758 144.76 143.30 -44.30
203 10315 362F 363S C N 2766 2768 -142.15 -136.60 7.28 0.23 -64.10 -173.76 19.07
203 363S 363S N CA 2768 2769 155.90 151.20 -35.00
204 10316 363S 364E C N 2772 2774 -80.97 -69.30 16.65 0.93 -63.60 166.23 23.13
204 364E 364E N CA 2774 2775 154.38 142.50 -40.30
205 10318 365I 366A C N 2789 2791 -126.48 -134.00 10.69 0.63 -62.50 176.50 32.35
205 366A 366A N CA 2791 2792 154.60 147.00 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 18 31 140 171 197 220 240 267 290 328
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: ASN:OXT ASN
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 350489
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -19009.3887
<< end of ENERGY.
DOPE score : -19009.388672
>> Model assessment by SOAP-Protein-OD score
preppdf_455W> None of the non-bonded terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3918541
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 999.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 0.0000
<< end of ENERGY.
SOAP-Protein-OD score : 0.000000
>> Model assessment by GA341 potential
Surface library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/surf5.de
Pair library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 62.856998
Sequence length : 367
Compactness : 0.011921
Native energy (pair) : 92.750579
Native energy (surface) : 58.330122
Native energy (combined) : 11.881281
Z score (pair) : -4.129315
Z score (surface) : 0.984446
Z score (combined) : -2.122395
GA341 score : 0.678443
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4697
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 2058.1731
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 2881 0 0 0.003 0.003 7.2587 1.000
2 Bond angle potential : 3935 0 1 1.705 1.705 214.41 1.000
3 Stereochemical cosine torsion poten: 1962 0 92 51.760 51.760 803.93 1.000
4 Stereochemical improper torsion pot: 1155 0 0 0.939 0.939 20.541 1.000
5 Soft-sphere overlap restraints : 4697 0 0 0.003 0.003 5.1733 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 765 0 8 1.447 1.447 113.62 1.000
10 Distance restraints 2 (N-O) : 973 0 12 1.596 1.596 151.96 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 366 0 0 2.853 2.853 35.120 1.000
14 Sidechain Chi_1 dihedral restraints: 315 0 0 84.607 84.607 92.544 1.000
15 Sidechain Chi_2 dihedral restraints: 209 0 1 74.590 74.590 83.937 1.000
16 Sidechain Chi_3 dihedral restraints: 98 0 0 81.062 81.062 51.484 1.000
17 Sidechain Chi_4 dihedral restraints: 34 0 0 105.174 105.174 22.703 1.000
18 Disulfide distance restraints : 5 0 0 0.004 0.004 0.13046E-01 1.000
19 Disulfide angle restraints : 10 0 0 2.119 2.119 0.99125 1.000
20 Disulfide dihedral angle restraints: 5 0 0 24.182 24.182 2.9986 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 643 0 2 0.632 0.632 28.250 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 365 209 47 36.563 135.382 386.62 1.000
26 Distance restraints 4 (SDCH-SDCH) : 183 0 0 2.147 2.147 36.618 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: WISP1.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 62327.9180
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 9954 1M 2R C N 7 9 -161.17 -125.20 41.80 1.24 -63.00 -174.85 31.56
1 2R 2R N CA 9 10 161.91 140.60 -41.10
2 9955 2R 3W C N 18 20 -72.29 -71.30 12.32 0.91 -63.00 164.79 21.18
2 3W 3W N CA 20 21 151.28 139.00 -44.20
3 9956 3W 4F C N 32 34 -83.34 -71.40 30.97 2.73 -63.20 157.71 20.58
3 4F 4F N CA 34 35 112.12 140.70 -44.30
4 9957 4F 5L C N 43 45 -129.99 -108.50 43.12 2.06 -63.50 163.08 26.76
4 5L 5L N CA 45 46 169.89 132.50 -41.20
5 9959 6P 7W C N 58 60 -89.94 -71.30 48.33 4.06 -63.00 141.20 16.26
5 7W 7W N CA 60 61 94.41 139.00 -44.20
6 9960 7W 8T C N 72 74 -153.61 -124.80 30.55 1.33 -63.20 -172.52 29.87
6 8T 8T N CA 74 75 153.66 143.50 -42.10
7 9961 8T 9L C N 79 81 -118.64 -108.50 12.77 0.71 -63.50 174.86 21.82
7 9L 9L N CA 81 82 124.74 132.50 -41.20
8 9962 9L 10A C N 87 89 -140.81 -134.00 8.06 0.19 -62.50 -174.83 34.54
8 10A 10A N CA 89 90 151.31 147.00 -40.90
9 9963 10A 11A C N 92 94 -115.71 -134.00 20.78 0.48 -62.50 -174.18 28.36
9 11A 11A N CA 94 95 137.14 147.00 -40.90
10 9965 12V 13T C N 104 106 -60.86 -78.10 34.21 1.12 -63.20 162.37 20.98
10 13T 13T N CA 106 107 120.25 149.80 -42.10
11 9966 13T 14A C N 111 113 -170.99 -134.00 49.29 1.38 -62.50 176.74 34.64
11 14A 14A N CA 113 114 179.58 147.00 -40.90
12 9967 14A 15A C N 116 118 -65.29 -68.20 5.02 0.49 -62.50 169.73 27.95
12 15A 15A N CA 118 119 149.39 145.30 -40.90
13 9968 15A 16A C N 121 123 -64.14 -68.20 7.01 0.68 -62.50 168.09 27.63
13 16A 16A N CA 123 124 151.02 145.30 -40.90
14 9969 16A 17A C N 126 128 -59.20 -68.20 22.44 1.51 -62.50 165.67 27.31
14 17A 17A N CA 128 129 124.74 145.30 -40.90
15 9970 17A 18S C N 131 133 165.98 -136.60 66.12 2.02 -64.10 -168.26 23.22
15 18S 18S N CA 133 134 -176.02 151.20 -35.00
16 9971 18S 19T C N 137 139 -81.39 -78.10 56.54 2.53 -63.20 136.67 16.39
16 19T 19T N CA 139 140 93.35 149.80 -42.10
17 9973 20V 21L C N 151 153 -63.64 -70.70 21.60 1.40 -63.50 162.39 22.54
17 21L 21L N CA 153 154 121.19 141.60 -41.20
18 9974 21L 22A C N 159 161 -169.79 -134.00 37.29 0.90 -62.50 -165.98 37.48
18 22A 22A N CA 161 162 157.44 147.00 -40.90
19 9976 23T 24A C N 171 173 -135.87 -134.00 8.49 0.43 -62.50 179.50 33.35
19 24A 24A N CA 173 174 155.28 147.00 -40.90
20 9977 24A 25L C N 176 178 -118.57 -108.50 11.79 0.52 -63.50 -171.92 23.59
20 25L 25L N CA 178 179 138.64 132.50 -41.20
21 9978 25L 26S C N 184 186 -122.03 -136.60 16.18 0.50 -64.10 -171.72 11.60
21 26S 26S N CA 186 187 144.15 151.20 -35.00
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44 70T 70T N CA 516 517 146.65 149.80 -42.10
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45 71D 71D N CA 523 524 -168.48 150.30 -40.00
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46 72G 72G N CA 531 532 151.48 -166.10 8.50
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67 107R 107R N CA 786 787 133.33 141.90 -41.10
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68 109R 109R N CA 804 805 138.20 141.90 -41.10
69 10062 109R 110Y C N 813 815 -132.79 -124.30 22.39 0.90 -63.50 174.80 31.17
69 110Y 110Y N CA 815 816 156.12 135.40 -43.40
70 10063 110Y 111A C N 825 827 -66.69 -68.20 2.43 0.15 -62.50 175.76 29.01
70 111A 111A N CA 827 828 143.39 145.30 -40.90
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71 113G 113G N CA 840 841 -153.21 174.10 8.50
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73 120G 120G N CA 885 886 150.11 174.10 8.50
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74 122G 122G N CA 896 897 122.22 174.10 8.50
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75 159R 159R N CA 1165 1166 154.03 140.60 -41.10
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77 164R 164R N CA 1208 1209 -150.16 140.60 -41.10
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78 166W 166W N CA 1227 1228 167.16 143.40 -44.20
79 10121 168P 169H C N 1252 1254 -53.02 -67.60 16.25 1.41 -63.20 170.82 20.74
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83 178H 178H N CA 1325 1326 130.40 140.00 -42.30
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84 181E 181E N CA 1347 1348 154.95 136.80 -40.30
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85 182Q 182Q N CA 1356 1357 112.04 140.70 -40.30
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89 187D 187D N CA 1401 1402 132.84 150.30 -40.00
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90 189A 189A N CA 1417 1418 128.20 145.30 -40.90
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91 191R 191R N CA 1431 1432 161.01 140.60 -41.10
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98 200T 200T N CA 1507 1508 163.28 143.50 -42.10
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99 201G 201G N CA 1514 1515 138.28 174.60 8.50
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101 203F 203F N CA 1523 1524 145.01 143.30 -44.30
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102 204D 204D N CA 1534 1535 115.36 114.20 -40.00
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103 205A 205A N CA 1542 1543 136.03 147.00 -40.90
104 10162 209V 210E C N 1572 1574 -107.71 -117.80 13.21 0.41 -63.60 174.26 21.13
104 210E 210E N CA 1574 1575 128.28 136.80 -40.30
105 10163 210E 211A C N 1581 1583 -68.09 -68.20 5.01 0.41 -62.50 168.88 27.95
105 211A 211A N CA 1583 1584 150.32 145.30 -40.90
106 10164 211A 212W C N 1586 1588 -63.37 -71.30 26.12 1.76 -63.00 158.31 19.77
106 212W 212W N CA 1588 1589 114.11 139.00 -44.20
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107 213H 213H N CA 1602 1603 129.99 138.80 -42.30
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108 214R 214R N CA 1612 1613 -173.90 140.60 -41.10
109 10167 214R 215N C N 1621 1623 -60.83 -71.20 10.55 0.81 -63.20 174.19 21.65
109 215N 215N N CA 1623 1624 144.72 142.80 -41.10
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110 216C 216C N CA 1631 1632 -43.07 -41.10 141.10
111 10170 217I 218A C N 1643 1645 160.94 -134.00 66.55 1.73 -62.50 -151.08 41.30
111 218A 218A N CA 1645 1646 160.99 147.00 -40.90
112 10171 218A 219Y C N 1648 1650 -118.54 -124.30 23.43 1.02 -63.50 165.51 23.75
112 219Y 219Y N CA 1650 1651 112.69 135.40 -43.40
113 10172 219Y 220T C N 1660 1662 -157.18 -63.20 107.75 18.56 -63.20 107.75 18.56
113 220T 220T N CA 1662 1663 -94.80 -42.10 -42.10
114 10173 220T 221S C N 1667 1669 -59.16 -72.40 13.47 0.88 -64.10 175.15 12.40
114 221S 221S N CA 1669 1670 149.92 152.40 -35.00
115 10175 222P 223W C N 1680 1682 58.49 -71.30 131.69 8.79 -63.00 -158.39 33.29
115 223W 223W N CA 1682 1683 116.69 139.00 -44.20
116 10176 223W 224S C N 1694 1696 -169.56 -136.60 44.83 1.42 -64.10 178.01 20.51
116 224S 224S N CA 1696 1697 -178.41 151.20 -35.00
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117 227S 227S N CA 1715 1716 160.88 151.20 -35.00
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118 228T 228T N CA 1721 1722 152.47 143.50 -42.10
119 10181 228T 229S C N 1726 1728 -137.72 -136.60 7.44 0.40 -64.10 -166.59 12.00
119 229S 229S N CA 1728 1729 143.85 151.20 -35.00
120 10183 230C 231G C N 1738 1740 -139.53 -167.20 47.58 1.27 82.20 -172.00 14.51
120 231G 231G N CA 1740 1741 135.89 174.60 8.50
121 10184 231G 232L C N 1742 1744 -133.49 -108.50 53.59 2.58 -63.50 155.52 25.92
121 232L 232L N CA 1744 1745 179.91 132.50 -41.20
122 10185 232L 233G C N 1750 1752 -67.44 -80.20 21.13 0.56 82.20 -149.00 6.62
122 233G 233G N CA 1752 1753 157.26 174.10 8.50
123 10187 234V 235S C N 1761 1763 -130.16 -136.60 12.17 0.69 -64.10 176.31 17.46
123 235S 235S N CA 1763 1764 161.53 151.20 -35.00
124 10188 235S 236T C N 1767 1769 -103.03 -124.80 55.32 1.81 -63.20 140.51 15.73
124 236T 236T N CA 1769 1770 92.65 143.50 -42.10
125 10189 236T 237R C N 1774 1776 176.99 -125.20 67.35 2.00 -63.00 -172.75 33.00
125 237R 237R N CA 1776 1777 175.16 140.60 -41.10
126 10191 238I 239S C N 1793 1795 -90.68 -72.40 39.37 1.82 -64.10 140.27 11.94
126 239S 239S N CA 1795 1796 -172.73 152.40 -35.00
127 10192 239S 240N C N 1799 1801 -60.92 -71.20 10.55 0.81 -63.20 173.76 21.60
127 240N 240N N CA 1801 1802 145.16 142.80 -41.10
128 10195 242N 243A C N 1822 1824 -59.76 -68.20 12.75 0.80 -62.50 176.66 29.09
128 243A 243A N CA 1824 1825 135.74 145.30 -40.90
129 10196 243A 244Q C N 1827 1829 -157.69 -121.10 44.21 1.37 -63.80 -178.62 31.46
129 244Q 244Q N CA 1829 1830 164.51 139.70 -40.30
130 10198 245C 246W C N 1842 1844 -65.95 -71.30 6.07 0.50 -63.00 173.96 21.93
130 246W 246W N CA 1844 1845 141.87 139.00 -44.20
131 10200 247P 248E C N 1863 1865 -125.75 -117.80 8.17 0.35 -63.60 -174.07 22.03
131 248E 248E N CA 1865 1866 134.93 136.80 -40.30
132 10201 248E 249Q C N 1872 1874 -132.31 -121.10 33.86 1.75 -63.80 163.13 21.17
132 249Q 249Q N CA 1874 1875 107.75 139.70 -40.30
133 10203 250E 251S C N 1890 1892 -124.91 -136.60 31.13 1.75 -64.10 157.19 15.71
133 251S 251S N CA 1892 1893 -179.96 151.20 -35.00
134 10204 251S 252R C N 1896 1898 -62.84 -72.10 11.90 1.03 -63.00 169.52 22.89
134 252R 252R N CA 1898 1899 149.38 141.90 -41.10
135 10205 252R 253L C N 1907 1909 -101.44 -108.50 28.10 1.58 -63.50 163.56 25.03
135 253L 253L N CA 1909 1910 159.70 132.50 -41.20
136 10207 254C 255N C N 1921 1923 -89.53 -71.20 31.89 2.50 -63.20 159.98 18.67
136 255N 255N N CA 1923 1924 116.70 142.80 -41.10
137 10208 255N 256L C N 1929 1931 -137.68 -108.50 31.83 1.41 -63.50 -171.25 30.80
137 256L 256L N CA 1931 1932 145.24 132.50 -41.20
138 10209 256L 257R C N 1937 1939 -74.44 -72.10 4.00 0.35 -63.00 -179.88 23.58
138 257R 257R N CA 1939 1940 138.66 141.90 -41.10
139 10212 259C 260D C N 1961 1963 -119.85 -96.50 34.85 1.43 -63.30 140.23 14.94
139 260D 260D N CA 1963 1964 88.33 114.20 -40.00
140 10213 260D 261V C N 1969 1971 -63.74 -62.40 10.96 1.47 -125.40 174.67 9.82
140 261V 261V N CA 1971 1972 -53.28 -42.40 143.30
141 10214 261V 262D C N 1976 1978 -118.78 -96.50 37.47 1.57 -63.30 -175.78 26.32
141 262D 262D N CA 1978 1979 144.33 114.20 -40.00
142 10216 263I 264H C N 1992 1994 -121.70 -125.60 19.48 0.66 -63.20 172.25 18.69
142 264H 264H N CA 1994 1995 119.71 138.80 -42.30
143 10217 264H 265T C N 2002 2004 -104.89 -124.80 38.67 1.20 -63.20 158.05 17.84
143 265T 265T N CA 2004 2005 110.35 143.50 -42.10
144 10218 265T 266L C N 2009 2011 -134.00 -108.50 25.53 1.20 -63.50 -171.38 23.28
144 266L 266L N CA 2011 2012 133.75 132.50 -41.20
145 10225 272K 273C C N 2061 2063 65.23 57.40 16.35 0.56 -117.90 -146.56 9.14
145 273C 273C N CA 2063 2064 21.64 36.00 141.10
146 10229 276V 277Y C N 2087 2089 -101.04 -98.40 34.26 3.62 -63.50 142.67 20.86
146 277Y 277Y N CA 2089 2090 94.24 128.40 -43.40
147 10230 277Y 278Q C N 2099 2101 -79.53 -73.00 31.82 1.95 -63.80 148.69 22.70
147 278Q 278Q N CA 2101 2102 171.84 140.70 -40.30
148 10232 279P 280E C N 2115 2117 -120.31 -117.80 7.08 0.30 -63.60 -174.82 27.90
148 280E 280E N CA 2117 2118 143.42 136.80 -40.30
149 10233 280E 281A C N 2124 2126 -122.21 -134.00 12.55 0.58 -62.50 178.09 32.38
149 281A 281A N CA 2126 2127 151.32 147.00 -40.90
150 10234 281A 282S C N 2129 2131 79.14 -136.60 145.87 5.25 -64.10 -150.98 16.49
150 282S 282S N CA 2131 2132 172.78 151.20 -35.00
151 10235 282S 283M C N 2135 2137 -110.20 -125.60 23.34 0.74 -63.40 170.04 22.21
151 283M 283M N CA 2137 2138 122.96 140.50 -40.50
152 10236 283M 284N C N 2143 2145 -123.29 -119.90 7.58 0.26 -63.20 -174.85 26.57
152 284N 284N N CA 2145 2146 143.78 137.00 -41.10
153 10239 286T 287L C N 2169 2171 91.89 -108.50 159.62 7.62 -63.50 -127.95 41.42
153 287L 287L N CA 2171 2172 131.13 132.50 -41.20
154 10240 287L 288A C N 2177 2179 -123.56 -134.00 10.69 0.28 -62.50 -175.19 33.55
154 288A 288A N CA 2179 2180 144.68 147.00 -40.90
155 10241 288A 289G C N 2182 2184 -64.29 -62.40 4.62 0.79 82.20 156.10 11.93
155 289G 289G N CA 2184 2185 -45.42 -41.20 8.50
156 10244 291I 292S C N 2200 2202 -80.85 -72.40 8.80 0.68 -64.10 175.84 13.81
156 292S 292S N CA 2202 2203 149.96 152.40 -35.00
157 10245 292S 293T C N 2206 2208 -114.06 -124.80 73.11 2.82 -63.20 124.18 13.33
157 293T 293T N CA 2208 2209 71.18 143.50 -42.10
158 10246 293T 294R C N 2213 2215 -163.69 -125.20 42.76 1.31 -63.00 -171.23 32.21
158 294R 294R N CA 2215 2216 159.22 140.60 -41.10
159 10247 294R 295S C N 2224 2226 -79.25 -72.40 9.88 0.47 -64.10 166.18 13.00
159 295S 295S N CA 2226 2227 159.52 152.40 -35.00
160 10248 295S 296Y C N 2230 2232 -118.67 -124.30 14.43 0.58 -63.50 174.47 25.14
160 296Y 296Y N CA 2232 2233 122.11 135.40 -43.40
161 10249 296Y 297Q C N 2242 2244 -120.51 -121.10 9.05 0.42 -63.80 -179.87 23.92
161 297Q 297Q N CA 2244 2245 130.67 139.70 -40.30
162 10251 298P 299K C N 2258 2260 -141.65 -118.00 38.31 1.42 -62.90 169.37 26.70
162 299K 299K N CA 2260 2261 169.25 139.10 -40.80
163 10252 299K 300Y C N 2267 2269 -106.90 -98.40 9.15 0.46 -63.50 173.93 25.52
163 300Y 300Y N CA 2269 2270 125.03 128.40 -43.40
164 10254 301C 302G C N 2285 2287 -71.24 -80.20 28.78 0.74 82.20 -153.47 6.86
164 302G 302G N CA 2287 2288 146.75 174.10 8.50
165 10257 304C 305M C N 2302 2304 -73.84 -73.00 38.68 2.60 -63.40 138.22 21.46
165 305M 305M N CA 2304 2305 -178.33 143.00 -40.50
166 10258 305M 306D C N 2310 2312 -60.75 -70.90 10.49 0.86 -63.30 167.07 20.47
166 306D 306D N CA 2312 2313 152.95 150.30 -40.00
167 10259 306D 307N C N 2318 2320 -125.03 -119.90 35.03 1.47 -63.20 159.71 23.47
167 307N 307N N CA 2320 2321 171.65 137.00 -41.10
168 10260 307N 308R C N 2326 2328 -115.83 -125.20 155.09 7.69 -125.20 155.09 7.69
168 308R 308R N CA 2328 2329 -64.60 140.60 140.60
169 10265 312P 313Y C N 2364 2366 -111.13 -98.40 12.74 0.50 -63.50 178.77 26.11
169 313Y 313Y N CA 2366 2367 128.91 128.40 -43.40
170 10266 313Y 314K C N 2376 2378 -81.46 -70.20 13.93 0.84 -62.90 171.60 23.34
170 314K 314K N CA 2378 2379 148.61 140.40 -40.80
171 10267 314K 315S C N 2385 2387 -66.91 -72.40 49.79 2.74 -64.10 137.95 9.83
171 315S 315S N CA 2387 2388 102.92 152.40 -35.00
172 10268 315S 316K C N 2391 2393 179.92 -118.00 71.51 2.37 -62.90 -173.87 31.01
172 316K 316K N CA 2393 2394 174.59 139.10 -40.80
173 10269 316K 317T C N 2400 2402 -87.44 -78.10 95.29 4.39 -63.20 100.05 11.40
173 317T 317T N CA 2402 2403 54.97 149.80 -42.10
174 10270 317T 318I C N 2407 2409 -65.89 -63.40 3.92 0.73 -120.60 -174.80 8.58
174 318I 318I N CA 2409 2410 -46.63 -43.60 130.30
175 10271 318I 319D C N 2415 2417 57.90 54.50 13.92 0.78 -63.30 138.67 23.68
175 319D 319D N CA 2417 2418 27.40 40.90 -40.00
176 10272 319D 320V C N 2423 2425 173.95 -125.40 83.07 2.28 -73.50 127.95 8.68
176 320V 320V N CA 2425 2426 -159.94 143.30 139.20
177 10278 325P 326D C N 2469 2471 -67.58 -96.50 30.23 1.24 -63.30 145.48 17.70
177 326D 326D N CA 2471 2472 105.41 114.20 -40.00
178 10279 326D 327G C N 2477 2479 -130.68 -167.20 37.22 0.57 82.20 -143.45 16.48
178 327G 327G N CA 2479 2480 167.41 174.60 8.50
179 10280 327G 328L C N 2481 2483 -102.09 -108.50 19.62 1.11 -63.50 172.14 26.26
179 328L 328L N CA 2483 2484 151.04 132.50 -41.20
180 10281 328L 329G C N 2489 2491 -73.84 -80.20 16.96 0.41 82.20 -143.64 6.92
180 329G 329G N CA 2491 2492 158.38 174.10 8.50
181 10282 329G 330F C N 2493 2495 -112.76 -124.20 12.74 0.65 -63.20 173.98 27.47
181 330F 330F N CA 2495 2496 148.92 143.30 -44.30
182 10283 330F 331S C N 2504 2506 -117.85 -136.60 18.75 0.76 -64.10 -178.53 16.89
182 331S 331S N CA 2506 2507 151.67 151.20 -35.00
183 10284 331S 332R C N 2510 2512 -121.64 -125.20 5.00 0.27 -63.00 -175.63 28.95
183 332R 332R N CA 2512 2513 144.10 140.60 -41.10
184 10285 332R 333Q C N 2521 2523 -106.76 -121.10 15.55 0.71 -63.80 179.19 28.64
184 333Q 333Q N CA 2523 2524 145.73 139.70 -40.30
185 10287 334V 335L C N 2537 2539 -140.09 -108.50 44.08 2.47 -63.50 162.19 19.87
185 335L 335L N CA 2539 2540 101.76 132.50 -41.20
186 10288 335L 336W C N 2545 2547 -142.44 -124.90 23.83 1.36 -63.00 -171.02 20.75
186 336W 336W N CA 2547 2548 127.27 143.40 -44.20
187 10290 337I 338N C N 2567 2569 -123.97 -119.90 22.61 1.11 -63.20 167.29 18.31
187 338N 338N N CA 2569 2570 114.76 137.00 -41.10
188 10291 338N 339A C N 2575 2577 -176.08 -134.00 42.18 1.29 -62.50 -156.16 39.42
188 339A 339A N CA 2577 2578 149.85 147.00 -40.90
189 10293 340C 341F C N 2586 2588 -126.31 -124.20 8.56 0.45 -63.20 -169.91 22.64
189 341F 341F N CA 2588 2589 135.01 143.30 -44.30
190 10295 342C 343N C N 2603 2605 -113.17 -119.90 24.91 0.96 -63.20 162.02 17.99
190 343N 343N N CA 2605 2606 113.02 137.00 -41.10
191 10296 343N 344L C N 2611 2613 -129.99 -108.50 23.91 1.27 -63.50 176.24 21.74
191 344L 344L N CA 2613 2614 122.01 132.50 -41.20
192 10297 344L 345S C N 2619 2621 -137.28 -136.60 10.42 0.54 -64.10 -169.58 11.83
192 345S 345S N CA 2621 2622 140.80 151.20 -35.00
193 10299 346C 347R C N 2631 2633 -132.20 -125.20 9.09 0.49 -63.00 -170.99 21.85
193 347R 347R N CA 2633 2634 134.79 140.60 -41.10
194 10300 347R 348N C N 2642 2644 -115.35 -119.90 27.15 1.12 -63.20 160.07 17.68
194 348N 348N N CA 2644 2645 110.24 137.00 -41.10
195 10302 349P 350N C N 2657 2659 -123.00 -119.90 15.19 0.75 -63.20 173.84 19.11
195 350N 350N N CA 2659 2660 122.13 137.00 -41.10
196 10303 350N 351D C N 2665 2667 -122.72 -96.50 28.31 1.15 -63.30 155.33 16.60
196 351D 351D N CA 2667 2668 103.52 114.20 -40.00
197 10305 352I 353F C N 2681 2683 -133.66 -124.20 9.46 0.37 -63.20 -173.85 30.46
197 353F 353F N CA 2683 2684 143.40 143.30 -44.30
198 10306 353F 354A C N 2692 2694 -148.63 -134.00 15.75 0.36 -62.50 -172.72 35.30
198 354A 354A N CA 2694 2695 152.81 147.00 -40.90
199 10307 354A 355D C N 2697 2699 -97.30 -96.50 5.03 0.21 -63.30 153.06 17.11
199 355D 355D N CA 2699 2700 109.24 114.20 -40.00
200 10308 355D 356L C N 2705 2707 -109.38 -108.50 1.64 0.08 -63.50 -178.99 22.94
200 356L 356L N CA 2707 2708 133.89 132.50 -41.20
201 10309 356L 357E C N 2713 2715 -118.82 -117.80 3.43 0.15 -63.60 -172.08 28.18
201 357E 357E N CA 2715 2716 140.07 136.80 -40.30
202 10310 357E 358S C N 2722 2724 -128.67 -136.60 9.60 0.51 -64.10 -179.65 17.63
202 358S 358S N CA 2724 2725 156.60 151.20 -35.00
203 10311 358S 359Y C N 2728 2730 -119.72 -124.30 7.99 0.32 -63.50 -178.81 26.15
203 359Y 359Y N CA 2730 2731 128.85 135.40 -43.40
204 10312 359Y 360P C N 2740 2742 -53.28 -58.70 6.53 0.56 -64.50 179.01 13.96
204 360P 360P N CA 2742 2743 -34.15 -30.50 147.20
205 10313 360P 361D C N 2747 2749 53.04 54.50 2.30 0.13 -63.30 142.72 24.25
205 361D 361D N CA 2749 2750 42.68 40.90 -40.00
206 10314 361D 362F C N 2755 2757 -109.16 -124.20 17.31 0.46 -63.20 -175.17 22.79
206 362F 362F N CA 2757 2758 134.73 143.30 -44.30
207 10315 362F 363S C N 2766 2768 -136.27 -136.60 6.97 0.36 -64.10 -178.22 18.31
207 363S 363S N CA 2768 2769 158.16 151.20 -35.00
208 10316 363S 364E C N 2772 2774 -73.68 -69.30 5.49 0.31 -63.60 174.18 23.78
208 364E 364E N CA 2774 2775 145.81 142.50 -40.30
209 10318 365I 366A C N 2789 2791 -121.64 -134.00 12.36 0.42 -62.50 -178.39 32.92
209 366A 366A N CA 2791 2792 147.39 147.00 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 23 36 156 179 237 229 268 272 327 335
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: ASN:OXT ASN
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 324540
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -17263.9219
<< end of ENERGY.
DOPE score : -17263.921875
>> Model assessment by SOAP-Protein-OD score
preppdf_455W> None of the non-bonded terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3918541
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 999.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 0.0000
<< end of ENERGY.
SOAP-Protein-OD score : 0.000000
>> Model assessment by GA341 potential
Surface library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/surf5.de
Pair library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 62.856998
Sequence length : 367
Compactness : 0.011363
Native energy (pair) : 175.468621
Native energy (surface) : 50.866196
Native energy (combined) : 13.135105
Z score (pair) : -1.120854
Z score (surface) : -0.510135
Z score (combined) : -1.080186
GA341 score : 0.329538
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4720
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 2089.6370
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 2881 0 0 0.003 0.003 6.9683 1.000
2 Bond angle potential : 3935 0 1 1.692 1.692 214.67 1.000
3 Stereochemical cosine torsion poten: 1962 0 80 51.281 51.281 785.63 1.000
4 Stereochemical improper torsion pot: 1155 0 0 0.935 0.935 21.334 1.000
5 Soft-sphere overlap restraints : 4720 0 0 0.003 0.003 5.7840 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 765 0 8 1.243 1.243 116.63 1.000
10 Distance restraints 2 (N-O) : 973 2 11 1.519 1.519 164.76 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 366 0 2 3.165 3.165 43.231 1.000
14 Sidechain Chi_1 dihedral restraints: 315 0 3 86.654 86.654 106.32 1.000
15 Sidechain Chi_2 dihedral restraints: 209 0 0 77.151 77.151 80.077 1.000
16 Sidechain Chi_3 dihedral restraints: 98 0 0 94.302 94.302 53.264 1.000
17 Sidechain Chi_4 dihedral restraints: 34 0 0 82.369 82.369 19.650 1.000
18 Disulfide distance restraints : 5 0 0 0.003 0.003 0.99187E-02 1.000
19 Disulfide angle restraints : 10 0 0 1.264 1.264 0.35293 1.000
20 Disulfide dihedral angle restraints: 5 0 0 34.888 34.888 4.9679 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 643 0 0 0.633 0.633 21.258 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 365 216 48 37.732 135.937 417.98 1.000
26 Distance restraints 4 (SDCH-SDCH) : 183 0 4 1.640 1.640 26.748 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: WISP1.V99990003
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 64216.6016
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 10 : Distance restraints 2 (N-O)
List of the RVIOL violations larger than : 4.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 12119 40E 148D N O 286 1102 8.49 5.54 2.95 4.52 5.54 2.95 4.52
2 12251 130Y 87C N O 951 641 4.77 2.66 2.11 4.62 2.66 2.11 4.62
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 9954 1M 2R C N 7 9 -129.55 -125.20 8.83 0.49 -63.00 -173.69 21.60
1 2R 2R N CA 9 10 132.92 140.60 -41.10
2 9955 2R 3W C N 18 20 -140.40 -124.90 19.23 0.61 -63.00 178.65 27.54
2 3W 3W N CA 20 21 154.79 143.40 -44.20
3 9956 3W 4F C N 32 34 -133.88 -124.20 11.21 0.58 -63.20 -168.44 31.24
3 4F 4F N CA 34 35 137.65 143.30 -44.30
4 9957 4F 5L C N 43 45 -142.28 -108.50 36.99 1.64 -63.50 -171.53 31.05
4 5L 5L N CA 45 46 147.58 132.50 -41.20
5 9959 6P 7W C N 58 60 -130.37 -124.90 10.11 0.35 -63.00 177.21 26.68
5 7W 7W N CA 60 61 151.90 143.40 -44.20
6 9960 7W 8T C N 72 74 -119.26 -124.80 5.55 0.29 -63.20 -176.73 27.23
6 8T 8T N CA 74 75 143.41 143.50 -42.10
7 9961 8T 9L C N 79 81 -107.31 -108.50 1.95 0.11 -63.50 -179.36 22.96
7 9L 9L N CA 81 82 134.05 132.50 -41.20
8 9962 9L 10A C N 87 89 -119.39 -134.00 14.78 0.41 -62.50 -176.64 33.08
8 10A 10A N CA 89 90 144.79 147.00 -40.90
9 9963 10A 11A C N 92 94 -113.24 -134.00 23.68 0.55 -62.50 -176.35 28.08
9 11A 11A N CA 94 95 135.60 147.00 -40.90
10 9965 12V 13T C N 104 106 -111.61 -124.80 23.80 0.74 -63.20 172.71 19.36
10 13T 13T N CA 106 107 123.69 143.50 -42.10
11 9966 13T 14A C N 111 113 -141.74 -134.00 8.07 0.20 -62.50 -172.57 34.96
11 14A 14A N CA 113 114 149.25 147.00 -40.90
12 9967 14A 15A C N 116 118 -129.41 -134.00 6.36 0.19 -62.50 -171.23 34.51
12 15A 15A N CA 118 119 142.59 147.00 -40.90
13 9968 15A 16A C N 121 123 -135.76 -134.00 2.18 0.06 -62.50 -174.13 34.38
13 16A 16A N CA 123 124 148.28 147.00 -40.90
14 9969 16A 17A C N 126 128 -117.19 -134.00 20.97 0.54 -62.50 -176.31 27.98
14 17A 17A N CA 128 129 134.46 147.00 -40.90
15 9970 17A 18S C N 131 133 46.97 -72.40 123.30 7.81 -64.10 -168.05 21.93
15 18S 18S N CA 133 134 121.54 152.40 -35.00
16 9971 18S 19T C N 137 139 -121.12 -124.80 4.64 0.16 -63.20 -173.55 27.76
16 19T 19T N CA 139 140 140.67 143.50 -42.10
17 9972 19T 20V C N 144 146 -62.19 -62.40 5.97 0.74 -125.40 179.81 10.11
17 20V 20V N CA 146 147 -48.36 -42.40 143.30
18 9973 20V 21L C N 151 153 -140.24 -108.50 32.76 1.48 -63.50 -166.00 31.69
18 21L 21L N CA 153 154 140.62 132.50 -41.20
19 9974 21L 22A C N 159 161 -63.01 -68.20 5.74 0.40 -62.50 176.25 28.91
19 22A 22A N CA 161 162 142.85 145.30 -40.90
20 9976 23T 24A C N 171 173 -153.74 -134.00 22.26 0.51 -62.50 -174.21 35.32
20 24A 24A N CA 173 174 157.27 147.00 -40.90
21 9977 24A 25L C N 176 178 -77.27 -70.70 20.10 1.30 -63.50 158.80 22.86
21 25L 25L N CA 178 179 160.59 141.60 -41.20
22 9978 25L 26S C N 184 186 -69.45 -72.40 10.16 0.70 -64.10 162.96 12.13
22 26S 26S N CA 186 187 162.13 152.40 -35.00
23 9980 27P 28A C N 197 199 -120.21 -134.00 13.87 0.52 -62.50 -179.92 32.59
23 28A 28A N CA 199 200 148.53 147.00 -40.90
24 9982 29P 30T C N 209 211 -91.87 -78.10 22.32 0.76 -63.20 153.24 21.56
24 30T 30T N CA 211 212 167.37 149.80 -42.10
25 9984 31T 32M C N 223 225 -71.79 -73.00 2.91 0.22 -63.40 174.06 26.65
25 32M 32M N CA 225 226 145.64 143.00 -40.50
26 9985 32M 33D C N 231 233 -99.25 -96.50 52.79 2.22 -63.30 107.66 11.62
26 33D 33D N CA 233 234 61.48 114.20 -40.00
27 9986 33D 34F C N 239 241 -138.39 -124.20 20.17 0.54 -63.20 175.04 29.16
27 34F 34F N CA 241 242 157.63 143.30 -44.30
28 9987 34F 35T C N 250 252 -79.43 -78.10 2.33 0.14 -63.20 170.79 22.98
28 35T 35T N CA 252 253 147.88 149.80 -42.10
29 9989 36P 37A C N 264 266 -96.43 -68.20 32.89 3.21 -62.50 172.70 26.84
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138 244Q 244Q N CA 1829 1830 169.79 139.70 -40.30
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141 10200 247P 248E C N 1863 1865 -128.81 -117.80 11.86 0.35 -63.60 -169.99 29.02
141 248E 248E N CA 1865 1866 141.23 136.80 -40.30
142 10201 248E 249Q C N 1872 1874 -129.21 -121.10 12.29 0.41 -63.80 -177.14 30.35
142 249Q 249Q N CA 1874 1875 148.93 139.70 -40.30
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143 250E 250E N CA 1883 1884 141.34 136.80 -40.30
144 10203 250E 251S C N 1890 1892 -131.01 -136.60 6.53 0.20 -64.10 -170.61 18.44
144 251S 251S N CA 1892 1893 147.82 151.20 -35.00
145 10204 251S 252R C N 1896 1898 -84.94 -72.10 14.87 0.99 -63.00 170.92 24.59
145 252R 252R N CA 1898 1899 149.40 141.90 -41.10
146 10205 252R 253L C N 1907 1909 -99.41 -108.50 20.38 0.99 -63.50 159.56 20.39
146 253L 253L N CA 1909 1910 114.27 132.50 -41.20
147 10207 254C 255N C N 1921 1923 -86.39 -71.20 43.12 3.18 -63.20 145.40 17.00
147 255N 255N N CA 1923 1924 102.44 142.80 -41.10
148 10208 255N 256L C N 1929 1931 -110.73 -108.50 11.10 0.62 -63.50 169.54 21.34
148 256L 256L N CA 1931 1932 121.63 132.50 -41.20
149 10209 256L 257R C N 1937 1939 -116.30 -125.20 22.85 0.88 -63.00 169.27 19.88
149 257R 257R N CA 1939 1940 119.56 140.60 -41.10
150 10212 259C 260D C N 1961 1963 -95.15 -70.90 54.89 1.84 -63.30 124.60 17.43
150 260D 260D N CA 1963 1964 -160.46 150.30 -40.00
151 10216 263I 264H C N 1992 1994 -70.74 -67.60 10.42 0.71 -63.20 167.94 21.47
151 264H 264H N CA 1994 1995 149.93 140.00 -42.30
152 10218 265T 266L C N 2009 2011 -79.69 -70.70 44.32 3.71 -63.50 140.34 18.62
152 266L 266L N CA 2011 2012 98.20 141.60 -41.20
153 10219 266L 267I C N 2017 2019 -67.28 -63.40 4.23 0.69 -120.60 -179.72 8.35
153 267I 267I N CA 2019 2020 -41.91 -43.60 130.30
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162 10238 285F 286T C N 2162 2164 -154.84 -124.80 50.26 1.56 -63.20 162.43 26.58
162 286T 286T N CA 2164 2165 -176.21 143.50 -42.10
163 10239 286T 287L C N 2169 2171 -69.56 -70.70 4.37 0.38 -63.50 173.09 24.38
163 287L 287L N CA 2171 2172 145.82 141.60 -41.20
164 10240 287L 288A C N 2177 2179 -66.85 -68.20 8.83 0.66 -62.50 177.53 28.88
164 288A 288A N CA 2179 2180 136.58 145.30 -40.90
165 10244 291I 292S C N 2200 2202 -151.58 -136.60 17.13 0.52 -64.10 -172.81 19.85
165 292S 292S N CA 2202 2203 159.51 151.20 -35.00
166 10245 292S 293T C N 2206 2208 -130.06 -124.80 13.05 0.42 -63.20 175.68 26.93
166 293T 293T N CA 2208 2209 155.44 143.50 -42.10
167 10246 293T 294R C N 2213 2215 -115.93 -125.20 13.22 0.40 -63.00 -179.78 21.32
167 294R 294R N CA 2215 2216 131.17 140.60 -41.10
168 10247 294R 295S C N 2224 2226 -86.41 -72.40 18.06 0.90 -64.10 162.73 13.25
168 295S 295S N CA 2226 2227 163.80 152.40 -35.00
169 10248 295S 296Y C N 2230 2232 -116.39 -124.30 19.94 0.80 -63.50 168.99 24.37
169 296Y 296Y N CA 2232 2233 117.10 135.40 -43.40
170 10249 296Y 297Q C N 2242 2244 -148.80 -121.10 30.05 1.38 -63.80 -171.43 24.36
170 297Q 297Q N CA 2244 2245 128.03 139.70 -40.30
171 10251 298P 299K C N 2258 2260 154.62 -118.00 88.96 3.11 -62.90 -143.22 36.40
171 299K 299K N CA 2260 2261 155.82 139.10 -40.80
172 10252 299K 300Y C N 2267 2269 -105.86 -98.40 23.95 2.40 -63.50 154.95 22.58
172 300Y 300Y N CA 2269 2270 105.64 128.40 -43.40
173 10254 301C 302G C N 2285 2287 -170.04 -167.20 26.71 1.07 82.20 176.30 13.11
173 302G 302G N CA 2287 2288 148.04 174.60 8.50
174 10257 304C 305M C N 2302 2304 -102.67 -125.60 22.99 0.95 -63.40 -178.45 30.24
174 305M 305M N CA 2304 2305 142.25 140.50 -40.50
175 10258 305M 306D C N 2310 2312 -67.85 -70.90 28.31 1.25 -63.30 162.22 19.75
175 306D 306D N CA 2312 2313 122.15 150.30 -40.00
176 10259 306D 307N C N 2318 2320 -135.86 -119.90 24.42 0.73 -63.20 178.85 26.47
176 307N 307N N CA 2320 2321 155.48 137.00 -41.10
177 10265 312P 313Y C N 2364 2366 -133.01 -124.30 52.40 2.42 -63.50 146.99 26.69
177 313Y 313Y N CA 2366 2367 -172.93 135.40 -43.40
178 10267 314K 315S C N 2385 2387 -93.62 -72.40 25.59 1.33 -64.10 161.03 13.64
178 315S 315S N CA 2387 2388 166.70 152.40 -35.00
179 10268 315S 316K C N 2391 2393 -82.88 -70.20 15.98 0.96 -62.90 170.26 23.25
179 316K 316K N CA 2393 2394 150.11 140.40 -40.80
180 10269 316K 317T C N 2400 2402 -119.94 -124.80 6.20 0.38 -63.20 179.75 26.82
180 317T 317T N CA 2402 2403 147.34 143.50 -42.10
181 10270 317T 318I C N 2407 2409 -64.76 -63.40 4.24 0.74 -120.60 -173.53 8.62
181 318I 318I N CA 2409 2410 -47.61 -43.60 130.30
182 10271 318I 319D C N 2415 2417 -91.02 -70.90 46.44 1.56 -63.30 130.82 17.92
182 319D 319D N CA 2417 2418 -167.85 150.30 -40.00
183 10272 319D 320V C N 2423 2425 -60.73 -62.40 7.50 0.87 -73.50 171.56 14.82
183 320V 320V N CA 2425 2426 -49.71 -42.40 139.20
184 10277 324C 325P C N 2462 2464 -49.15 -58.70 31.32 1.94 -64.50 153.25 12.26
184 325P 325P N CA 2464 2465 -60.32 -30.50 147.20
185 10278 325P 326D C N 2469 2471 178.23 -96.50 96.54 4.00 -63.30 -160.49 32.08
185 326D 326D N CA 2471 2472 159.48 114.20 -40.00
186 10279 326D 327G C N 2477 2479 -149.62 -167.20 22.54 0.44 82.20 -161.17 14.96
186 327G 327G N CA 2479 2480 160.49 174.60 8.50
187 10280 327G 328L C N 2481 2483 -106.87 -108.50 1.68 0.08 -63.50 179.41 22.81
187 328L 328L N CA 2483 2484 132.89 132.50 -41.20
188 10281 328L 329G C N 2489 2491 -155.02 -167.20 48.44 1.71 82.20 171.13 13.16
188 329G 329G N CA 2491 2492 127.71 174.60 8.50
189 10282 329G 330F C N 2493 2495 -146.70 -124.20 23.61 0.72 -63.20 -174.88 31.06
189 330F 330F N CA 2495 2496 150.48 143.30 -44.30
190 10283 330F 331S C N 2504 2506 -126.82 -136.60 18.07 0.66 -64.10 -177.85 11.23
190 331S 331S N CA 2506 2507 136.01 151.20 -35.00
191 10284 331S 332R C N 2510 2512 -128.69 -125.20 4.45 0.13 -63.00 -172.58 29.84
191 332R 332R N CA 2512 2513 143.37 140.60 -41.10
192 10285 332R 333Q C N 2521 2523 -106.82 -121.10 21.25 0.71 -63.80 169.80 22.94
192 333Q 333Q N CA 2523 2524 123.95 139.70 -40.30
193 10287 334V 335L C N 2537 2539 -115.60 -108.50 12.57 0.72 -63.50 171.44 21.45
193 335L 335L N CA 2539 2540 122.13 132.50 -41.20
194 10288 335L 336W C N 2545 2547 -130.07 -124.90 6.78 0.38 -63.00 -170.92 28.13
194 336W 336W N CA 2547 2548 139.02 143.40 -44.20
195 10290 337I 338N C N 2567 2569 -123.13 -119.90 8.92 0.47 -63.20 -179.95 19.85
195 338N 338N N CA 2569 2570 128.69 137.00 -41.10
196 10291 338N 339A C N 2575 2577 -170.16 -134.00 37.87 0.91 -62.50 -166.44 37.42
196 339A 339A N CA 2577 2578 158.25 147.00 -40.90
197 10293 340C 341F C N 2586 2588 -115.35 -124.20 19.39 0.66 -63.20 178.15 21.55
197 341F 341F N CA 2588 2589 126.05 143.30 -44.30
198 10295 342C 343N C N 2603 2605 -123.08 -119.90 10.31 0.53 -63.20 178.63 19.69
198 343N 343N N CA 2605 2606 127.20 137.00 -41.10
199 10296 343N 344L C N 2611 2613 -117.92 -108.50 14.19 0.80 -63.50 171.93 21.45
199 344L 344L N CA 2613 2614 121.89 132.50 -41.20
200 10297 344L 345S C N 2619 2621 -140.03 -136.60 5.24 0.29 -64.10 -166.70 19.40
200 345S 345S N CA 2621 2622 147.24 151.20 -35.00
201 10300 347R 348N C N 2642 2644 42.51 55.90 29.52 1.41 -63.20 150.35 24.28
201 348N 348N N CA 2644 2645 65.81 39.50 -41.10
202 10302 349P 350N C N 2657 2659 -101.21 -119.90 27.14 0.80 -63.20 162.92 18.53
202 350N 350N N CA 2659 2660 117.32 137.00 -41.10
203 10303 350N 351D C N 2665 2667 -126.84 -96.50 30.89 1.27 -63.30 172.17 18.45
203 351D 351D N CA 2667 2668 120.02 114.20 -40.00
204 10305 352I 353F C N 2681 2683 -137.04 -124.20 14.10 0.39 -63.20 -177.80 30.10
204 353F 353F N CA 2683 2684 149.13 143.30 -44.30
205 10306 353F 354A C N 2692 2694 -141.56 -134.00 9.43 0.24 -62.50 -175.70 34.44
205 354A 354A N CA 2694 2695 152.62 147.00 -40.90
206 10307 354A 355D C N 2697 2699 -95.07 -96.50 19.31 0.81 -63.30 138.63 15.46
206 355D 355D N CA 2699 2700 94.95 114.20 -40.00
207 10308 355D 356L C N 2705 2707 -111.44 -108.50 3.15 0.14 -63.50 -178.70 22.91
207 356L 356L N CA 2707 2708 133.65 132.50 -41.20
208 10309 356L 357E C N 2713 2715 -110.96 -117.80 10.06 0.33 -63.60 176.22 21.26
208 357E 357E N CA 2715 2716 129.43 136.80 -40.30
209 10310 357E 358S C N 2722 2724 -139.07 -136.60 5.29 0.21 -64.10 -175.01 18.74
209 358S 358S N CA 2724 2725 155.87 151.20 -35.00
210 10311 358S 359Y C N 2728 2730 -118.87 -124.30 8.56 0.36 -63.50 -179.13 26.13
210 359Y 359Y N CA 2730 2731 128.78 135.40 -43.40
211 10312 359Y 360P C N 2740 2742 -53.51 -58.70 6.80 0.52 -64.50 178.24 13.89
211 360P 360P N CA 2742 2743 -34.90 -30.50 147.20
212 10313 360P 361D C N 2747 2749 -80.08 -70.90 19.57 0.65 -63.30 153.35 19.98
212 361D 361D N CA 2749 2750 167.58 150.30 -40.00
213 10314 361D 362F C N 2755 2757 -111.67 -124.20 18.57 1.03 -63.20 165.93 26.27
213 362F 362F N CA 2757 2758 157.01 143.30 -44.30
214 10315 362F 363S C N 2766 2768 -66.27 -72.40 6.16 0.42 -64.10 173.15 12.67
214 363S 363S N CA 2768 2769 151.86 152.40 -35.00
215 10316 363S 364E C N 2772 2774 -74.13 -69.30 7.02 0.39 -63.60 172.42 23.57
215 364E 364E N CA 2774 2775 147.60 142.50 -40.30
216 10318 365I 366A C N 2789 2791 -104.06 -134.00 30.33 0.83 -62.50 -178.18 31.99
216 366A 366A N CA 2791 2792 142.10 147.00 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 25 42 190 183 231 254 243 280 299 342
<< end of ENERGY.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: ASN:OXT ASN
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 331609
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -18903.2168
<< end of ENERGY.
DOPE score : -18903.216797
>> Model assessment by SOAP-Protein-OD score
preppdf_455W> None of the non-bonded terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3918541
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 999.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 0.0000
<< end of ENERGY.
SOAP-Protein-OD score : 0.000000
>> Model assessment by GA341 potential
Surface library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/surf5.de
Pair library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 62.856998
Sequence length : 367
Compactness : 0.011643
Native energy (pair) : 99.628431
Native energy (surface) : 50.079533
Native energy (combined) : 10.995486
Z score (pair) : -3.520322
Z score (surface) : -0.720860
Z score (combined) : -2.664887
GA341 score : 0.857862
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4507
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1996.5691
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 2881 0 0 0.003 0.003 6.6816 1.000
2 Bond angle potential : 3935 0 3 1.640 1.640 200.08 1.000
3 Stereochemical cosine torsion poten: 1962 0 88 51.526 51.526 788.63 1.000
4 Stereochemical improper torsion pot: 1155 0 1 0.953 0.953 21.110 1.000
5 Soft-sphere overlap restraints : 4507 0 0 0.003 0.003 5.5781 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 765 1 6 1.395 1.395 132.41 1.000
10 Distance restraints 2 (N-O) : 973 0 21 1.720 1.720 192.56 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 366 0 1 2.707 2.707 31.630 1.000
14 Sidechain Chi_1 dihedral restraints: 315 0 2 87.603 87.603 92.354 1.000
15 Sidechain Chi_2 dihedral restraints: 209 0 1 71.017 71.017 67.644 1.000
16 Sidechain Chi_3 dihedral restraints: 98 0 0 90.528 90.528 53.214 1.000
17 Sidechain Chi_4 dihedral restraints: 34 0 0 99.471 99.471 21.859 1.000
18 Disulfide distance restraints : 5 0 0 0.008 0.008 0.51672E-01 1.000
19 Disulfide angle restraints : 10 0 0 1.767 1.767 0.68951 1.000
20 Disulfide dihedral angle restraints: 5 0 0 29.188 29.188 4.0229 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 643 0 0 0.585 0.585 16.124 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 365 196 42 33.960 129.879 352.14 1.000
26 Distance restraints 4 (SDCH-SDCH) : 183 0 0 1.529 1.529 9.7950 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: WISP1.V99990004
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 60087.8203
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 9954 1M 2R C N 7 9 -140.34 -125.20 17.98 0.95 -63.00 -171.43 21.58
1 2R 2R N CA 9 10 130.89 140.60 -41.10
2 9955 2R 3W C N 18 20 -146.45 -124.90 24.38 0.81 -63.00 -178.65 28.29
2 3W 3W N CA 20 21 154.79 143.40 -44.20
3 9956 3W 4F C N 32 34 -104.48 -124.20 28.31 0.77 -63.20 172.31 21.33
3 4F 4F N CA 34 35 122.99 143.30 -44.30
4 9957 4F 5L C N 43 45 -117.30 -108.50 15.91 0.91 -63.50 169.23 21.10
4 5L 5L N CA 45 46 119.25 132.50 -41.20
5 9959 6P 7W C N 58 60 -146.12 -124.90 24.53 0.80 -63.00 -179.61 28.15
5 7W 7W N CA 60 61 155.70 143.40 -44.20
6 9960 7W 8T C N 72 74 -126.11 -124.80 8.05 0.31 -63.20 177.95 26.98
6 8T 8T N CA 74 75 151.44 143.50 -42.10
7 9961 8T 9L C N 79 81 -102.40 -108.50 8.49 0.38 -63.50 172.24 22.00
7 9L 9L N CA 81 82 126.59 132.50 -41.20
8 9962 9L 10A C N 87 89 -121.80 -134.00 17.10 0.51 -62.50 -174.36 28.18
8 10A 10A N CA 89 90 135.02 147.00 -40.90
9 9963 10A 11A C N 92 94 -77.14 -68.20 9.52 0.90 -62.50 177.66 29.86
9 11A 11A N CA 94 95 142.05 145.30 -40.90
10 9965 12V 13T C N 104 106 -105.66 -124.80 71.58 2.53 -63.20 124.11 13.59
10 13T 13T N CA 106 107 74.52 143.50 -42.10
11 9966 13T 14A C N 111 113 -164.78 -134.00 31.36 0.83 -62.50 -164.92 37.41
11 14A 14A N CA 113 114 152.98 147.00 -40.90
12 9967 14A 15A C N 116 118 -77.63 -68.20 11.42 0.75 -62.50 168.03 28.30
12 15A 15A N CA 118 119 151.75 145.30 -40.90
13 9968 15A 16A C N 121 123 -115.84 -134.00 18.33 0.52 -62.50 -177.40 32.76
13 16A 16A N CA 123 124 144.47 147.00 -40.90
14 9969 16A 17A C N 126 128 -94.93 -68.20 35.54 3.51 -62.50 165.98 25.81
14 17A 17A N CA 128 129 121.88 145.30 -40.90
15 9970 17A 18S C N 131 133 -174.21 -136.60 44.45 1.35 -64.10 -173.83 21.44
15 18S 18S N CA 133 134 174.89 151.20 -35.00
16 9971 18S 19T C N 137 139 -120.87 -124.80 17.77 0.88 -63.20 167.32 25.27
16 19T 19T N CA 139 140 160.83 143.50 -42.10
17 9974 21L 22A C N 159 161 -130.28 -134.00 3.72 0.12 -62.50 -174.94 33.96
17 22A 22A N CA 161 162 146.90 147.00 -40.90
18 9976 23T 24A C N 171 173 -154.88 -134.00 23.15 0.53 -62.50 -173.41 35.51
18 24A 24A N CA 173 174 156.98 147.00 -40.90
19 9978 25L 26S C N 184 186 -163.32 -136.60 27.85 1.31 -64.10 -155.91 13.30
19 26S 26S N CA 186 187 143.35 151.20 -35.00
20 9980 27P 28A C N 197 199 -70.71 -68.20 5.61 0.53 -62.50 179.01 29.75
20 28A 28A N CA 199 200 140.28 145.30 -40.90
21 9983 30T 31T C N 216 218 -118.93 -124.80 12.49 0.70 -63.20 172.62 25.83
21 31T 31T N CA 218 219 154.52 143.50 -42.10
22 9984 31T 32M C N 223 225 -85.30 -73.00 18.85 1.48 -63.40 170.63 23.85
22 32M 32M N CA 225 226 128.72 143.00 -40.50
23 9985 32M 33D C N 231 233 -112.12 -96.50 24.91 1.02 -63.30 143.37 15.45
23 33D 33D N CA 233 234 94.80 114.20 -40.00
24 9989 36P 37A C N 264 266 -160.04 -134.00 27.11 0.66 -62.50 -168.71 36.55
24 37A 37A N CA 266 267 154.55 147.00 -40.90
25 9992 39L 40E C N 284 286 -124.11 -117.80 40.71 2.14 -69.30 71.50 6.56
25 40E 40E N CA 286 287 96.58 136.80 142.50
26 9993 40E 41D C N 293 295 -70.24 -70.90 20.52 0.98 -63.30 169.93 20.56
26 41D 41D N CA 295 296 129.79 150.30 -40.00
27 9994 41D 42T C N 301 303 -109.56 -124.80 43.39 1.45 -63.20 152.21 16.90
27 42T 42T N CA 303 304 102.87 143.50 -42.10
28 9997 44S 45R C N 320 322 -66.80 -72.10 11.56 0.78 -63.00 172.76 23.09
28 45R 45R N CA 322 323 131.62 141.90 -41.10
29 9999 46P 47Q C N 338 340 -155.05 -121.10 34.09 1.35 -63.80 -160.89 25.70
29 47Q 47Q N CA 340 341 136.67 139.70 -40.30
30 10000 47Q 48F C N 347 349 -122.38 -124.20 3.89 0.13 -63.20 -174.47 29.69
30 48F 48F N CA 349 350 139.87 143.30 -44.30
31 10002 49C 50K C N 364 366 -76.21 -70.20 6.06 0.42 -62.90 178.48 23.93
31 50K 50K N CA 366 367 141.22 140.40 -40.80
32 10003 50K 51W C N 373 375 -91.81 -71.30 22.65 1.38 -63.00 169.66 23.07
32 51W 51W N CA 375 376 148.61 139.00 -44.20
33 10004 51W 52P C N 387 389 -66.06 -58.70 9.60 0.74 -64.50 171.54 12.88
33 52P 52P N CA 389 390 -24.33 -30.50 147.20
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112 228T 228T N CA 1721 1722 132.17 149.80 -42.10
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114 231G 231G N CA 1740 1741 132.51 174.10 8.50
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115 232L 232L N CA 1744 1745 152.44 141.60 -41.20
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116 233G 233G N CA 1752 1753 158.17 174.10 8.50
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119 10189 236T 237R C N 1774 1776 -115.39 -125.20 20.05 1.11 -63.00 169.14 26.47
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121 240N 240N N CA 1801 1802 156.51 137.00 -41.10
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122 242N 242N N CA 1816 1817 143.14 137.00 -41.10
123 10195 242N 243A C N 1822 1824 -116.65 -134.00 21.38 0.54 -62.50 -176.43 27.97
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124 10196 243A 244Q C N 1827 1829 -148.26 -121.10 34.85 1.09 -63.80 179.30 30.73
124 244Q 244Q N CA 1829 1830 161.53 139.70 -40.30
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125 246W 246W N CA 1844 1845 -179.97 143.40 -44.20
126 10200 247P 248E C N 1863 1865 -76.86 -69.30 14.22 0.83 -63.60 165.68 22.83
126 248E 248E N CA 1865 1866 154.55 142.50 -40.30
127 10201 248E 249Q C N 1872 1874 -67.60 -73.00 7.53 0.44 -63.80 175.80 25.65
127 249Q 249Q N CA 1874 1875 135.45 140.70 -40.30
128 10202 249Q 250E C N 1881 1883 -146.34 -117.80 47.99 1.69 -63.60 166.35 26.75
128 250E 250E N CA 1883 1884 175.38 136.80 -40.30
129 10203 250E 251S C N 1890 1892 -72.58 -72.40 21.17 1.24 -64.10 151.67 11.51
129 251S 251S N CA 1892 1893 173.57 152.40 -35.00
130 10204 251S 252R C N 1896 1898 -75.89 -72.10 60.95 4.77 -63.00 122.84 15.76
130 252R 252R N CA 1898 1899 81.06 141.90 -41.10
131 10207 254C 255N C N 1921 1923 -113.81 -119.90 12.79 0.68 -63.20 178.00 25.14
131 255N 255N N CA 1923 1924 148.25 137.00 -41.10
132 10209 256L 257R C N 1937 1939 -121.81 -125.20 26.90 1.37 -63.00 162.62 26.01
132 257R 257R N CA 1939 1940 167.28 140.60 -41.10
133 10211 258P 259C C N 1955 1957 -61.76 -63.00 6.96 0.77 -117.90 179.93 7.77
133 259C 259C N CA 1957 1958 -47.95 -41.10 141.10
134 10212 259C 260D C N 1961 1963 -97.23 -96.50 13.38 0.56 -63.30 170.96 19.29
134 260D 260D N CA 1963 1964 127.56 114.20 -40.00
135 10214 261V 262D C N 1976 1978 -91.76 -70.90 59.77 2.09 -63.30 117.21 16.30
135 262D 262D N CA 1978 1979 -153.69 150.30 -40.00
136 10216 263I 264H C N 1992 1994 -129.10 -125.60 4.44 0.11 -63.20 -171.91 27.83
136 264H 264H N CA 1994 1995 141.53 138.80 -42.30
137 10218 265T 266L C N 2009 2011 -134.55 -108.50 27.82 1.24 -63.50 -169.70 30.82
137 266L 266L N CA 2011 2012 142.26 132.50 -41.20
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158 10259 306D 307N C N 2318 2320 -107.24 -119.90 19.78 1.07 -63.20 172.42 24.06
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165 327G 327G N CA 2479 2480 147.46 174.60 8.50
166 10280 327G 328L C N 2481 2483 -106.19 -108.50 6.48 0.37 -63.50 -175.24 23.57
166 328L 328L N CA 2483 2484 138.56 132.50 -41.20
167 10281 328L 329G C N 2489 2491 -168.48 -167.20 10.06 0.41 82.20 -169.41 13.96
167 329G 329G N CA 2491 2492 164.62 174.60 8.50
168 10282 329G 330F C N 2493 2495 -130.93 -124.20 25.30 1.01 -63.20 162.77 26.99
168 330F 330F N CA 2495 2496 167.69 143.30 -44.30
169 10283 330F 331S C N 2504 2506 -60.82 -72.40 12.58 0.73 -64.10 177.56 12.67
169 331S 331S N CA 2506 2507 147.47 152.40 -35.00
170 10284 331S 332R C N 2510 2512 -101.34 -125.20 29.41 0.87 -63.00 168.91 20.51
170 332R 332R N CA 2512 2513 123.40 140.60 -41.10
171 10285 332R 333Q C N 2521 2523 -135.39 -121.10 14.46 0.59 -63.80 -168.33 25.10
171 333Q 333Q N CA 2523 2524 137.50 139.70 -40.30
172 10287 334V 335L C N 2537 2539 -120.25 -108.50 22.06 1.26 -63.50 165.09 20.48
172 335L 335L N CA 2539 2540 113.83 132.50 -41.20
173 10288 335L 336W C N 2545 2547 -136.76 -124.90 15.09 0.85 -63.00 -167.08 21.23
173 336W 336W N CA 2547 2548 134.06 143.40 -44.20
174 10290 337I 338N C N 2567 2569 -131.83 -119.90 23.51 1.26 -63.20 172.12 18.70
174 338N 338N N CA 2569 2570 116.74 137.00 -41.10
175 10291 338N 339A C N 2575 2577 -159.81 -134.00 25.92 0.77 -62.50 -164.34 37.26
175 339A 339A N CA 2577 2578 149.36 147.00 -40.90
176 10293 340C 341F C N 2586 2588 -120.27 -124.20 14.88 0.59 -63.20 -177.59 21.89
176 341F 341F N CA 2588 2589 128.96 143.30 -44.30
177 10295 342C 343N C N 2603 2605 -114.32 -119.90 9.65 0.30 -63.20 177.74 19.85
177 343N 343N N CA 2605 2606 129.13 137.00 -41.10
178 10296 343N 344L C N 2611 2613 -107.04 -108.50 7.19 0.37 -63.50 172.26 21.83
178 344L 344L N CA 2613 2614 125.46 132.50 -41.20
179 10297 344L 345S C N 2619 2621 -131.60 -136.60 12.63 0.52 -64.10 -172.81 11.57
179 345S 345S N CA 2621 2622 139.60 151.20 -35.00
180 10299 346C 347R C N 2631 2633 -123.19 -125.20 5.15 0.20 -63.00 -173.09 21.90
180 347R 347R N CA 2633 2634 135.86 140.60 -41.10
181 10300 347R 348N C N 2642 2644 -106.62 -119.90 25.34 0.82 -63.20 162.43 18.26
181 348N 348N N CA 2644 2645 115.42 137.00 -41.10
182 10302 349P 350N C N 2657 2659 -104.48 -119.90 19.45 0.57 -63.20 171.30 19.43
182 350N 350N N CA 2659 2660 125.15 137.00 -41.10
183 10303 350N 351D C N 2665 2667 -109.18 -96.50 62.19 2.60 -63.30 103.99 11.04
183 351D 351D N CA 2667 2668 53.32 114.20 -40.00
184 10305 352I 353F C N 2681 2683 -120.17 -124.20 10.42 0.38 -63.20 -173.11 22.50
184 353F 353F N CA 2683 2684 133.69 143.30 -44.30
185 10306 353F 354A C N 2692 2694 -139.38 -134.00 5.38 0.18 -62.50 -171.51 35.01
185 354A 354A N CA 2694 2695 147.00 147.00 -40.90
186 10307 354A 355D C N 2697 2699 -104.52 -96.50 12.37 0.51 -63.30 150.53 16.53
186 355D 355D N CA 2699 2700 104.78 114.20 -40.00
187 10308 355D 356L C N 2705 2707 -101.71 -108.50 15.56 0.76 -63.50 164.21 20.94
187 356L 356L N CA 2707 2708 118.51 132.50 -41.20
188 10309 356L 357E C N 2713 2715 -132.94 -117.80 15.34 0.50 -63.60 -167.47 22.67
188 357E 357E N CA 2715 2716 139.31 136.80 -40.30
189 10310 357E 358S C N 2722 2724 -132.95 -136.60 4.92 0.16 -64.10 -169.99 18.63
189 358S 358S N CA 2724 2725 147.90 151.20 -35.00
190 10311 358S 359Y C N 2728 2730 -118.06 -124.30 10.80 0.43 -63.50 178.52 25.79
190 359Y 359Y N CA 2730 2731 126.58 135.40 -43.40
191 10312 359Y 360P C N 2740 2742 -53.26 -58.70 7.44 0.54 -64.50 177.58 13.85
191 360P 360P N CA 2742 2743 -35.58 -30.50 147.20
192 10313 360P 361D C N 2747 2749 -98.45 -96.50 11.01 0.46 -63.30 168.74 18.97
192 361D 361D N CA 2749 2750 125.04 114.20 -40.00
193 10314 361D 362F C N 2755 2757 -110.18 -124.20 17.77 0.46 -63.20 -177.17 22.46
193 362F 362F N CA 2757 2758 132.39 143.30 -44.30
194 10315 362F 363S C N 2766 2768 -138.23 -136.60 8.65 0.40 -64.10 -178.83 18.41
194 363S 363S N CA 2768 2769 159.69 151.20 -35.00
195 10316 363S 364E C N 2772 2774 -77.03 -69.30 13.77 0.79 -63.60 166.34 22.92
195 364E 364E N CA 2774 2775 153.90 142.50 -40.30
196 10318 365I 366A C N 2789 2791 -71.81 -68.20 9.16 0.62 -62.50 165.64 27.61
196 366A 366A N CA 2791 2792 153.72 145.30 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 1 21 51 166 161 193 215 258 264 295 322
<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
>> Model assessment by DOPE potential
iatmcls_286W> MODEL atom not classified: ASN:OXT ASN
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 321041
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 1 9999
NLOGN_USE : 15
CONTACT_SHELL : 15.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F T
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : -19025.3555
<< end of ENERGY.
DOPE score : -19025.355469
>> Model assessment by SOAP-Protein-OD score
preppdf_455W> None of the non-bonded terms selected.
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 3918541
Dynamic pairs routine : 1, NATM x NATM double loop
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 999.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T F F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 0.0000
<< end of ENERGY.
SOAP-Protein-OD score : 0.000000
>> Model assessment by GA341 potential
Surface library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/surf5.de
Pair library : /Users/yingyinli/opt/anaconda3/lib/modeller-10.1/modlib/pair9.de
Chain identifier : _
% sequence identity : 62.856998
Sequence length : 367
Compactness : 0.013353
Native energy (pair) : 78.545624
Native energy (surface) : 48.121285
Native energy (combined) : 10.186766
Z score (pair) : -3.183653
Z score (surface) : -0.856761
Z score (combined) : -2.831354
GA341 score : 0.900786
>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL : 367
Number of all, selected real atoms : 2804 2804
Number of all, selected pseudo atoms : 0 0
Number of all static, selected restraints : 13904 13904
COVALENT_CYS : F
NONBONDED_SEL_ATOMS : 1
Number of non-bonded pairs (excluding 1-2,1-3,1-4): 4280
Dynamic pairs routine : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) : 0.390
LENNARD_JONES_SWITCH : 6.500 7.500
COULOMB_JONES_SWITCH : 6.500 7.500
RESIDUE_SPAN_RANGE : 0 99999
NLOGN_USE : 15
CONTACT_SHELL : 4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER : T T F F F
SPHERE_STDV : 0.050
RADII_FACTOR : 0.820
Current energy : 1910.7992
Summary of the restraint violations:
NUM ... number of restraints.
NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
RVIOL ... relative difference from the best value.
NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB).
RMS_2 ... RMS(feature, best_value, NUMB).
MOL.PDF ... scaled contribution to -Ln(Molecular pdf).
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i
------------------------------------------------------------------------------------------------------
1 Bond length potential : 2881 0 0 0.003 0.003 5.6976 1.000
2 Bond angle potential : 3935 0 1 1.657 1.657 207.49 1.000
3 Stereochemical cosine torsion poten: 1962 0 76 50.892 50.892 778.76 1.000
4 Stereochemical improper torsion pot: 1155 0 0 0.879 0.879 18.661 1.000
5 Soft-sphere overlap restraints : 4280 0 0 0.003 0.003 3.2089 1.000
6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000
7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000
8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000
9 Distance restraints 1 (CA-CA) : 765 0 7 1.210 1.210 92.864 1.000
10 Distance restraints 2 (N-O) : 973 0 14 1.659 1.659 170.22 1.000
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
13 Mainchain Omega dihedral restraints: 366 0 1 2.941 2.941 37.329 1.000
14 Sidechain Chi_1 dihedral restraints: 315 0 1 82.890 82.890 77.825 1.000
15 Sidechain Chi_2 dihedral restraints: 209 0 0 69.614 69.614 72.752 1.000
16 Sidechain Chi_3 dihedral restraints: 98 0 0 92.088 92.088 56.170 1.000
17 Sidechain Chi_4 dihedral restraints: 34 0 0 115.214 115.214 20.919 1.000
18 Disulfide distance restraints : 5 0 0 0.007 0.007 0.38949E-01 1.000
19 Disulfide angle restraints : 10 0 0 1.934 1.934 0.82595 1.000
20 Disulfide dihedral angle restraints: 5 0 0 37.626 37.626 5.7777 1.000
21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
23 Distance restraints 3 (SDCH-MNCH) : 643 0 0 0.606 0.606 17.365 1.000
24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000
25 Phi/Psi pair of dihedral restraints: 365 200 38 32.046 131.145 321.50 1.000
26 Distance restraints 4 (SDCH-SDCH) : 183 0 2 1.406 1.406 23.393 1.000
27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000
30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000
31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000
32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000
33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000
34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000
35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000
36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000
37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000
38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000
39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000
# Heavy relative violation of each residue is written to: WISP1.V99990005
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues: 1
# The sum of all numbers in the file: 60767.0391
List of the violated restraints:
A restraint is violated when the relative difference
from the best value (RVIOL) is larger than CUTOFF.
ICSR ... index of a restraint in the current set.
RESNO ... residue numbers of the first two atoms.
ATM ... IUPAC atom names of the first two atoms.
FEAT ... the value of the feature in the model.
restr ... the mean of the basis restraint with the smallest
difference from the model (local minimum).
viol ... difference from the local minimum.
rviol ... relative difference from the local minimum.
RESTR ... the best value (global minimum).
VIOL ... difference from the best value.
RVIOL ... relative difference from the best value.
-------------------------------------------------------------------------------------------------
Feature 25 : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than : 6.5000
# ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL
1 9955 2R 3W C N 18 20 -63.37 -71.30 12.56 0.75 -63.00 173.46 21.66
1 3W 3W N CA 20 21 129.26 139.00 -44.20
2 9956 3W 4F C N 32 34 -123.32 -124.20 15.20 0.69 -63.20 -177.39 21.77
2 4F 4F N CA 34 35 128.13 143.30 -44.30
3 9957 4F 5L C N 43 45 -86.94 -70.70 20.54 1.38 -63.50 166.29 24.50
3 5L 5L N CA 45 46 154.17 141.60 -41.20
4 9959 6P 7W C N 58 60 -113.55 -124.90 12.14 0.43 -63.00 -176.19 26.33
4 7W 7W N CA 60 61 139.08 143.40 -44.20
5 9960 7W 8T C N 72 74 -91.66 -78.10 27.42 0.90 -63.20 147.06 20.76
5 8T 8T N CA 74 75 173.62 149.80 -42.10
6 9961 8T 9L C N 79 81 -98.73 -108.50 9.81 0.46 -63.50 176.43 22.72
6 9L 9L N CA 81 82 131.67 132.50 -41.20
7 9962 9L 10A C N 87 89 -135.73 -134.00 6.43 0.32 -62.50 -178.65 33.64
7 10A 10A N CA 89 90 153.19 147.00 -40.90
8 9963 10A 11A C N 92 94 -104.32 -134.00 33.94 0.78 -62.50 176.46 27.19
8 11A 11A N CA 94 95 130.54 147.00 -40.90
9 9965 12V 13T C N 104 106 -125.06 -124.80 10.35 0.45 -63.20 -174.15 20.42
9 13T 13T N CA 106 107 133.15 143.50 -42.10
10 9966 13T 14A C N 111 113 -153.36 -134.00 21.15 0.48 -62.50 -172.86 35.52
10 14A 14A N CA 113 114 155.50 147.00 -40.90
11 9967 14A 15A C N 116 118 -133.15 -134.00 1.68 0.07 -62.50 -172.61 34.49
11 15A 15A N CA 118 119 145.54 147.00 -40.90
12 9968 15A 16A C N 121 123 -140.67 -134.00 11.36 0.41 -62.50 -179.30 33.80
12 16A 16A N CA 123 124 156.19 147.00 -40.90
13 9969 16A 17A C N 126 128 -89.46 -68.20 34.16 3.34 -62.50 161.73 25.32
13 17A 17A N CA 128 129 118.57 145.30 -40.90
14 9970 17A 18S C N 131 133 -169.78 -136.60 34.58 1.14 -64.10 -164.86 21.76
14 18S 18S N CA 133 134 160.95 151.20 -35.00
15 9971 18S 19T C N 137 139 -103.03 -124.80 69.23 2.37 -63.20 126.32 13.97
15 19T 19T N CA 139 140 77.78 143.50 -42.10
16 9974 21L 22A C N 159 161 -110.28 -134.00 24.18 0.64 -62.50 -176.87 32.54
16 22A 22A N CA 161 162 142.31 147.00 -40.90
17 9975 22A 23T C N 164 166 -69.59 -78.10 19.41 0.64 -63.20 174.58 21.97
17 23T 23T N CA 166 167 132.36 149.80 -42.10
18 9976 23T 24A C N 171 173 -73.77 -68.20 6.40 0.43 -62.50 171.01 28.59
18 24A 24A N CA 173 174 148.46 145.30 -40.90
19 9978 25L 26S C N 184 186 -133.83 -136.60 7.61 0.32 -64.10 -167.80 11.88
19 26S 26S N CA 186 187 144.11 151.20 -35.00
20 9979 26S 27P C N 190 192 -74.00 -58.70 31.69 1.85 -64.50 150.25 11.72
20 27P 27P N CA 192 193 -2.75 -30.50 147.20
21 9983 30T 31T C N 216 218 -94.31 -78.10 30.16 0.99 -63.20 146.02 20.80
21 31T 31T N CA 218 219 175.23 149.80 -42.10
22 9984 31T 32M C N 223 225 -93.08 -73.00 27.02 2.15 -63.40 168.06 22.94
22 32M 32M N CA 225 226 124.92 143.00 -40.50
23 9985 32M 33D C N 231 233 -83.40 -70.90 18.78 0.72 -63.30 156.98 20.64
23 33D 33D N CA 233 234 164.31 150.30 -40.00
24 9987 34F 35T C N 250 252 -131.76 -124.80 7.30 0.43 -63.20 -170.57 28.82
24 35T 35T N CA 252 253 141.32 143.50 -42.10
25 9989 36P 37A C N 264 266 -131.75 -134.00 2.25 0.07 -62.50 -174.43 34.12
25 37A 37A N CA 266 267 146.94 147.00 -40.90
26 9991 38P 39L C N 276 278 -78.50 -70.70 17.08 1.07 -63.50 162.69 23.48
26 39L 39L N CA 278 279 156.80 141.60 -41.20
27 9992 39L 40E C N 284 286 -59.35 -63.60 5.86 0.70 -69.30 173.44 13.58
27 40E 40E N CA 286 287 -44.34 -40.30 142.50
28 9994 41D 42T C N 301 303 -79.58 -78.10 65.51 2.85 -63.20 127.46 15.32
28 42T 42T N CA 303 304 84.31 149.80 -42.10
29 9997 44S 45R C N 320 322 -95.89 -72.10 25.51 2.13 -63.00 176.87 21.86
29 45R 45R N CA 322 323 132.69 141.90 -41.10
30 9999 46P 47Q C N 338 340 -112.82 -121.10 8.99 0.41 -63.80 -176.81 29.55
30 47Q 47Q N CA 340 341 143.19 139.70 -40.30
31 10000 47Q 48F C N 347 349 -117.16 -124.20 13.10 0.41 -63.20 -175.37 22.34
31 48F 48F N CA 349 350 132.26 143.30 -44.30
32 10001 48F 49C C N 358 360 -65.75 -63.00 6.90 1.05 -117.90 179.23 7.70
32 49C 49C N CA 360 361 -47.42 -41.10 141.10
33 10002 49C 50K C N 364 366 -79.74 -70.20 9.58 0.72 -62.90 -179.59 24.38
33 50K 50K N CA 366 367 139.57 140.40 -40.80
34 10003 50K 51W C N 373 375 -111.51 -124.90 15.94 0.51 -63.00 -174.59 20.87
34 51W 51W N CA 375 376 134.75 143.40 -44.20
35 10006 53C 54E C N 400 402 -60.40 -69.30 10.05 0.60 -63.60 178.17 23.93
35 54E 54E N CA 402 403 137.84 142.50 -40.30
36 10010 57P 58S C N 429 431 -76.02 -72.40 4.91 0.24 -64.10 169.69 13.04
36 58S 58S N CA 431 432 155.72 152.40 -35.00
37 10013 60P 61R C N 449 451 -149.62 -125.20 24.61 0.91 -63.00 -164.54 32.30
37 61R 61R N CA 451 452 143.68 140.60 -41.10
38 10016 63P 64L C N 473 475 -101.48 -108.50 10.80 0.61 -63.50 -177.90 27.60
38 64L 64L N CA 475 476 140.70 132.50 -41.20
39 10017 64L 65G C N 481 483 85.30 78.70 19.32 0.31 82.20 167.27 8.28
39 65G 65G N CA 483 484 175.74 -166.10 8.50
40 10019 66V 67S C N 492 494 -114.79 -136.60 35.83 1.25 -64.10 165.71 10.21
40 67S 67S N CA 494 495 122.76 151.20 -35.00
41 10020 67S 68L C N 498 500 -123.95 -108.50 15.65 0.78 -63.50 -178.44 22.57
41 68L 68L N CA 500 501 130.00 132.50 -41.20
42 10022 69I 70T C N 514 516 -122.59 -124.80 8.03 0.41 -63.20 176.95 26.62
42 70T 70T N CA 516 517 151.22 143.50 -42.10
43 10023 70T 71D C N 521 523 -72.91 -70.90 2.02 0.16 -63.30 170.13 21.59
43 71D 71D N CA 523 524 150.14 150.30 -40.00
44 10024 71D 72G C N 529 531 -171.39 -167.20 13.20 0.45 82.20 -152.09 14.81
44 72G 72G N CA 531 532 -172.88 174.60 8.50
45 10026 73C 74E C N 539 541 -119.08 -117.80 10.86 0.52 -63.60 -179.17 27.25
45 74E 74E N CA 541 542 147.58 136.80 -40.30
46 10028 75C 76C C N 554 556 -64.88 -63.00 3.17 0.52 -117.90 -176.92 7.87
46 76C 76C N CA 556 557 -43.66 -41.10 141.10
47 10030 77K 78M C N 569 571 -82.11 -73.00 13.05 1.03 -63.40 175.15 24.75
47 78M 78M N CA 571 572 133.65 143.00 -40.50
48 10032 79C 80A C N 583 585 -61.30 -68.20 7.00 0.55 -62.50 175.00 28.62
48 80A 80A N CA 585 586 144.11 145.30 -40.90
49 10033 80A 81Q C N 588 590 -85.98 -73.00 13.26 0.99 -63.80 179.68 25.30
49 81Q 81Q N CA 590 591 138.00 140.70 -40.30
50 10034 81Q 82Q C N 597 599 -132.20 -121.10 12.33 0.58 -63.80 -172.45 24.61
50 82Q 82Q N CA 599 600 134.33 139.70 -40.30
51 10040 87C 88T C N 640 642 -135.83 -124.80 24.75 0.79 -63.20 168.68 26.37
51 88T 88T N CA 642 643 165.66 143.50 -42.10
52 10041 88T 89E C N 647 649 -166.43 -117.80 53.42 1.57 -63.60 -169.14 31.07
52 89E 89E N CA 649 650 158.91 136.80 -40.30
53 10042 89E 90A C N 656 658 166.76 -134.00 67.00 1.54 -62.50 -167.86 38.19
53 90A 90A N CA 658 659 178.29 147.00 -40.90
54 10043 90A 91A C N 661 663 -69.66 -68.20 6.99 0.51 -62.50 167.12 27.74
54 91A 91A N CA 663 664 152.14 145.30 -40.90
55 10046 93C 94D C N 680 682 -119.42 -96.50 24.98 1.03 -63.30 173.47 18.78
55 94D 94D N CA 682 683 124.15 114.20 -40.00
56 10048 95P 96H C N 695 697 -108.66 -125.60 46.77 1.43 -63.20 144.82 15.83
56 96H 96H N CA 697 698 95.20 138.80 -42.30
57 10049 96H 97R C N 705 707 -165.55 -125.20 51.33 1.52 -63.00 178.88 30.92
57 97R 97R N CA 707 708 172.34 140.60 -41.10
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115 231G 231G N CA 1740 1741 143.16 174.10 8.50
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123 10194 241V 242N C N 1814 1816 -171.53 -119.90 82.84 2.51 -63.20 159.54 25.63
123 242N 242N N CA 1816 1817 -158.22 137.00 -41.10
124 10195 242N 243A C N 1822 1824 -63.04 -68.20 9.23 0.89 -62.50 166.14 27.25
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125 10196 243A 244Q C N 1827 1829 -60.95 -73.00 17.77 1.03 -63.80 167.96 24.85
125 244Q 244Q N CA 1829 1830 127.64 140.70 -40.30
126 10198 245C 246W C N 1842 1844 -94.99 -71.30 40.67 3.50 -63.00 153.51 17.57
126 246W 246W N CA 1844 1845 105.95 139.00 -44.20
127 10200 247P 248E C N 1863 1865 -77.44 -69.30 8.18 0.59 -63.60 176.93 24.36
127 248E 248E N CA 1865 1866 143.31 142.50 -40.30
128 10201 248E 249Q C N 1872 1874 -124.21 -121.10 15.93 0.70 -63.80 175.13 28.95
128 249Q 249Q N CA 1874 1875 155.32 139.70 -40.30
129 10202 249Q 250E C N 1881 1883 -67.65 -69.30 2.50 0.14 -63.60 179.12 24.10
129 250E 250E N CA 1883 1884 140.62 142.50 -40.30
130 10203 250E 251S C N 1890 1892 -115.61 -136.60 45.66 1.78 -64.10 154.49 9.52
130 251S 251S N CA 1892 1893 110.65 151.20 -35.00
131 10204 251S 252R C N 1896 1898 -132.51 -63.00 102.50 11.97 -63.00 102.50 11.97
131 252R 252R N CA 1898 1899 34.23 -41.10 -41.10
132 10205 252R 253L C N 1907 1909 -142.35 -108.50 40.63 1.79 -63.50 -178.18 30.12
132 253L 253L N CA 1909 1910 154.97 132.50 -41.20
133 10207 254C 255N C N 1921 1923 -151.89 -119.90 36.83 1.11 -63.20 -173.86 28.24
133 255N 255N N CA 1923 1924 155.25 137.00 -41.10
134 10208 255N 256L C N 1929 1931 -124.72 -108.50 28.32 1.32 -63.50 174.18 27.97
134 256L 256L N CA 1931 1932 155.73 132.50 -41.20
135 10209 256L 257R C N 1937 1939 -67.77 -72.10 9.13 0.61 -63.00 175.03 23.33
135 257R 257R N CA 1939 1940 133.86 141.90 -41.10
136 10212 259C 260D C N 1961 1963 -66.17 -70.90 15.34 0.55 -63.30 175.72 21.52
136 260D 260D N CA 1963 1964 135.70 150.30 -40.00
137 10214 261V 262D C N 1976 1978 -67.46 -70.90 3.64 0.23 -63.30 170.94 21.35
137 262D 262D N CA 1978 1979 149.12 150.30 -40.00
138 10216 263I 264H C N 1992 1994 -174.23 -125.60 75.49 1.91 -63.20 164.34 27.36
138 264H 264H N CA 1994 1995 -163.46 138.80 -42.30
139 10217 264H 265T C N 2002 2004 -63.95 -78.10 34.13 1.12 -63.20 160.84 20.58
139 265T 265T N CA 2004 2005 118.74 149.80 -42.10
140 10218 265T 266L C N 2009 2011 -98.30 -108.50 45.37 2.33 -63.50 134.09 16.96
140 266L 266L N CA 2011 2012 88.29 132.50 -41.20
141 10225 272K 273C C N 2061 2063 -61.86 -63.00 9.06 1.03 -117.90 177.87 7.68
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188 351D 351D N CA 2667 2668 158.83 150.30 -40.00
189 10305 352I 353F C N 2681 2683 -129.82 -124.20 12.79 0.70 -63.20 -171.70 22.24
189 353F 353F N CA 2683 2684 131.82 143.30 -44.30
190 10306 353F 354A C N 2692 2694 -147.48 -134.00 16.11 0.86 -62.50 -161.77 29.74
190 354A 354A N CA 2694 2695 138.19 147.00 -40.90
191 10307 354A 355D C N 2697 2699 -131.99 -96.50 52.45 2.15 -63.30 134.45 14.29
191 355D 355D N CA 2699 2700 75.59 114.20 -40.00
192 10308 355D 356L C N 2705 2707 -116.32 -108.50 13.11 0.61 -63.50 -176.46 28.74
192 356L 356L N CA 2707 2708 143.03 132.50 -41.20
193 10309 356L 357E C N 2713 2715 -113.65 -117.80 14.86 0.66 -63.60 170.35 20.40
193 357E 357E N CA 2715 2716 122.53 136.80 -40.30
194 10310 357E 358S C N 2722 2724 -138.69 -136.60 10.20 0.55 -64.10 -168.64 11.90
194 358S 358S N CA 2724 2725 141.22 151.20 -35.00
195 10311 358S 359Y C N 2728 2730 -122.61 -124.30 16.69 0.81 -63.50 172.64 24.71
195 359Y 359Y N CA 2730 2731 118.80 135.40 -43.40
196 10313 360P 361D C N 2747 2749 -131.29 -96.50 44.99 1.84 -63.30 142.89 15.16
196 361D 361D N CA 2749 2750 85.68 114.20 -40.00
197 10314 361D 362F C N 2755 2757 -136.66 -124.20 18.55 0.51 -63.20 174.84 29.04
197 362F 362F N CA 2757 2758 157.04 143.30 -44.30
198 10315 362F 363S C N 2766 2768 -113.34 -136.60 25.52 0.79 -64.10 -177.53 11.30
198 363S 363S N CA 2768 2769 140.69 151.20 -35.00
199 10316 363S 364E C N 2772 2774 -76.33 -69.30 12.14 0.69 -63.60 167.78 23.08
199 364E 364E N CA 2774 2775 152.40 142.50 -40.30
200 10318 365I 366A C N 2789 2791 -143.47 -134.00 23.35 1.03 -62.50 171.13 32.37
200 366A 366A N CA 2791 2792 168.34 147.00 -40.90
report______> Distribution of short non-bonded contacts:
DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY: 0 0 0 0 0 16 41 139 145 183 217 249 235 295 288
<< end of ENERGY.
>> Summary of successfully produced models:
Filename molpdf DOPE score GA341 score SOAP-Protein-OD score
--------------------------------------------------------------------------------------------
WISP1.B99990001.pdb 2115.55103 -19561.43750 0.97372 0.00000
WISP1.B99990002.pdb 2058.17310 -19009.38867 0.67844 0.00000
WISP1.B99990003.pdb 2089.63696 -17263.92188 0.32954 0.00000
WISP1.B99990004.pdb 1996.56909 -18903.21680 0.85786 0.00000
WISP1.B99990005.pdb 1910.79919 -19025.35547 0.90079 0.00000
#read in and display the PDB file of the model generated from homology modeling
mdl_v = ngv.show_structure_file('WISP1.B99990001.pdb')
mdl_v.display()
mdl_v.render_image();
mdl_v._display_image()
PyMOL (https://pymol.org/2/) is a molecular visualization system which can be used to visualize PDB file for protein structures. It can also be used for making structural biology analysis such as align molecules imported as different PDB files.
HawkDock (http://cadd.zju.edu.cn/hawkdock/) is a free and open accessed web server developed to predict and analyze the structures of protein and protein interactions. It could be used to predict binding structures (output as a series of PDB files) of a receptor and a ligand submitted as PDB files and identify key residues of protein and protein interaction.
Note on Data analysis method
The alternative method to using online web server for investigating molecular docking is to build our own machine learning models for prediction, which is out of scope for this class (had been cleared by the professer to use online web servers for analysis of molecular docking prediction as it is better suited for my hypothesis)
Method: After constructing the model from homology modeling, submit the model PDB file to PDBsum to generate a Ramachandran plot analysis to evaluate the validity of the protein structure. The result (in a URL) should arrive within 48 hours after submitting work to the server. You would need the passward sent to you in the email you left on the server to access the PDBsum data of your structure.
The online webserver PDBsum: http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html
Here is the result page that the URL should direct you to:
Click on PROCHECK to obtain the Ramachandran plot analysis. Here is what you should see as the Main Ramachandran plot.
For our homology modeling structure, 81.9% of residues are in the most favoured regions, 13.2% residues are in the additional allowed regions, 3.5% residues are in the generously allowed regions, with only 1.3% of residues being in the disallowed regions. Now we would proceed to do interaction analysis using this model we generated.
After evaluating the model, submit the model PDB file to protein-protein interaction web server for analysis of general binding sites.
The online web server meta-PPISP: https://pipe.rcc.fsu.edu/meta-ppisp/
After submitting the PDB file to the web server, the result should arrive within a couple of hours. After obtaining the result output sent to the email you left on the web server, which containing interface prediction data in pdb file, upload the PDB file to the Jupyter notebook and analyze results
#load the web server output PDB files from local directories as regular PDB files using read_pdb
ppdb = PandasPdb()
ppdb.read_pdb('000029356.pdb')
#After loading a PDB file from the local directory, the PandasPdb.df attribute should contain the 4 DataFrame objects
#'ATOM': contains the entries from the ATOM coordinate section
#'HETATM': contains entries from the "HETATM" coordinate section
#'ANISOU': contains entries from the "ANISOU" coordinate section
#'OTHERS': Everything else that is not a 'ATOM', 'HETATM', or 'ANISOU' entry
#note: some PDB files may only contain HETATM or ATOM entries
ppdb.df.keys()
dict_keys(['ATOM', 'HETATM', 'ANISOU', 'OTHERS'])
#The output PDB file we receive only contain the ATOM entries, so we will build our dataframe based on ATOM entries record
#data_list is a global variable
data_list = ppdb.df['ATOM']
#code check
data_list.head()
| record_name | atom_number | blank_1 | atom_name | alt_loc | residue_name | blank_2 | chain_id | residue_number | insertion | ... | x_coord | y_coord | z_coord | occupancy | b_factor | blank_4 | segment_id | element_symbol | charge | line_idx | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | ATOM | 1 | N | MET | A | 1 | ... | -10.306 | -10.013 | 28.782 | 1.0 | 0.06 | NaN | 0 | |||||||
| 1 | ATOM | 2 | CA | MET | A | 1 | ... | -11.181 | -9.105 | 29.550 | 1.0 | 0.06 | NaN | 1 | |||||||
| 2 | ATOM | 3 | CB | MET | A | 1 | ... | -11.081 | -9.407 | 31.059 | 1.0 | 0.06 | NaN | 2 | |||||||
| 3 | ATOM | 4 | CG | MET | A | 1 | ... | -11.597 | -10.784 | 31.485 | 1.0 | 0.06 | NaN | 3 | |||||||
| 4 | ATOM | 5 | SD | MET | A | 1 | ... | -13.402 | -10.988 | 31.398 | 1.0 | 0.06 | NaN | 4 |
5 rows × 21 columns
#Setting the residue number as the dataframe index to better visualize data
#interface_prediction is a global variable
interface_prediction = pd.DataFrame(data_list).set_index('residue_number')
#code check
interface_prediction.head()
| record_name | atom_number | blank_1 | atom_name | alt_loc | residue_name | blank_2 | chain_id | insertion | blank_3 | x_coord | y_coord | z_coord | occupancy | b_factor | blank_4 | segment_id | element_symbol | charge | line_idx | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| residue_number | ||||||||||||||||||||
| 1 | ATOM | 1 | N | MET | A | -10.306 | -10.013 | 28.782 | 1.0 | 0.06 | NaN | 0 | ||||||||
| 1 | ATOM | 2 | CA | MET | A | -11.181 | -9.105 | 29.550 | 1.0 | 0.06 | NaN | 1 | ||||||||
| 1 | ATOM | 3 | CB | MET | A | -11.081 | -9.407 | 31.059 | 1.0 | 0.06 | NaN | 2 | ||||||||
| 1 | ATOM | 4 | CG | MET | A | -11.597 | -10.784 | 31.485 | 1.0 | 0.06 | NaN | 3 | ||||||||
| 1 | ATOM | 5 | SD | MET | A | -13.402 | -10.988 | 31.398 | 1.0 | 0.06 | NaN | 4 |
#As stated in the document for meta-PPISP (in the email you would receive), meta-PPSIP prediction scores are stored as B-factors in the PDB file output we received
#We will be filtering for residue names and B-factor values as the most relevant data for our purpose
#interface_prediction_sorted is a global variable
interface_prediction_sorted = interface_prediction[['residue_name', 'b_factor']]
#code check
interface_prediction_sorted.head()
| residue_name | b_factor | |
|---|---|---|
| residue_number | ||
| 1 | MET | 0.06 |
| 1 | MET | 0.06 |
| 1 | MET | 0.06 |
| 1 | MET | 0.06 |
| 1 | MET | 0.06 |
from biopandas.pdb import PandasPdb
#create a dictionary where the key is the residue number and the ouput is the b-factor based on the dataframe parsed from the PDB file
#prediction_dict is a global variable
prediction_dict = dict([(i,[a,b]) for i,a,b in zip(interface_prediction_sorted.index, interface_prediction_sorted.residue_name,interface_prediction_sorted.b_factor)])
#code check
prediction_dict
{1: ['MET', 0.06],
2: ['ARG', 0.1],
3: ['TRP', 0.16],
4: ['PHE', 0.08],
5: ['LEU', 0.1],
6: ['PRO', 0.18],
7: ['TRP', 0.12],
8: ['THR', 0.06],
9: ['LEU', 0.1],
10: ['ALA', 0.07],
11: ['ALA', 0.02],
12: ['VAL', 0.03],
13: ['THR', 0.07],
14: ['ALA', 0.05],
15: ['ALA', 0.05],
16: ['ALA', 0.14],
17: ['ALA', 0.19],
18: ['SER', 0.1],
19: ['THR', 0.07],
20: ['VAL', 0.09],
21: ['LEU', 0.02],
22: ['ALA', 0.05],
23: ['THR', 0.04],
24: ['ALA', 0.03],
25: ['LEU', 0.1],
26: ['SER', 0.05],
27: ['PRO', 0.03],
28: ['ALA', 0.05],
29: ['PRO', 0.04],
30: ['THR', 0.04],
31: ['THR', 0.03],
32: ['MET', 0.06],
33: ['ASP', 0.05],
34: ['PHE', 0.04],
35: ['THR', 0.02],
36: ['PRO', 0.04],
37: ['ALA', 0.03],
38: ['PRO', 0.02],
39: ['LEU', 0.02],
40: ['GLU', 0.03],
41: ['ASP', 0.05],
42: ['THR', 0.06],
43: ['SER', 0.05],
44: ['SER', 0.05],
45: ['ARG', 0.05],
46: ['PRO', 0.04],
47: ['GLN', 0.05],
48: ['PHE', 0.1],
49: ['CYS', 0.12],
50: ['LYS', 0.05],
51: ['TRP', 0.14],
52: ['PRO', 0.15],
53: ['CYS', 0.09],
54: ['GLU', 0.16],
55: ['CYS', 0.15],
56: ['PRO', 0.12],
57: ['PRO', 0.12],
58: ['SER', 0.1],
59: ['PRO', 0.11],
60: ['PRO', 0.12],
61: ['ARG', 0.14],
62: ['CYS', 0.06],
63: ['PRO', 0.05],
64: ['LEU', 0.06],
65: ['GLY', 0.08],
66: ['VAL', 0.05],
67: ['SER', 0.04],
68: ['LEU', 0.07],
69: ['ILE', 0.04],
70: ['THR', 0.11],
71: ['ASP', 0.08],
72: ['GLY', 0.08],
73: ['CYS', 0.19],
74: ['GLU', 0.21],
75: ['CYS', 0.14],
76: ['CYS', 0.19],
77: ['LYS', 0.23],
78: ['MET', 0.2],
79: ['CYS', 0.14],
80: ['ALA', 0.21],
81: ['GLN', 0.03],
82: ['GLN', 0.04],
83: ['LEU', 0.04],
84: ['GLY', 0.0],
85: ['ASP', 0.0],
86: ['ASN', 0.05],
87: ['CYS', 0.0],
88: ['THR', 0.09],
89: ['GLU', 0.0],
90: ['ALA', 0.0],
91: ['ALA', 0.13],
92: ['ILE', 0.14],
93: ['CYS', 0.16],
94: ['ASP', 0.17],
95: ['PRO', 0.19],
96: ['HIS', 0.19],
97: ['ARG', 0.12],
98: ['GLY', 0.2],
99: ['LEU', 0.22],
100: ['TYR', 0.14],
101: ['CYS', 0.26],
102: ['ASP', 0.22],
103: ['TYR', 0.2],
104: ['SER', 0.14],
105: ['GLY', 0.14],
106: ['ASP', 0.07],
107: ['ARG', 0.09],
108: ['PRO', 0.1],
109: ['ARG', 0.08],
110: ['TYR', 0.09],
111: ['ALA', 0.1],
112: ['ILE', 0.05],
113: ['GLY', 0.05],
114: ['VAL', 0.07],
115: ['CYS', 0.05],
116: ['ALA', 0.04],
117: ['GLN', 0.06],
118: ['VAL', 0.07],
119: ['VAL', 0.09],
120: ['GLY', 0.0],
121: ['VAL', 0.1],
122: ['GLY', 0.09],
123: ['CYS', 0.1],
124: ['VAL', 0.17],
125: ['LEU', 0.17],
126: ['ASP', 0.16],
127: ['GLY', 0.19],
128: ['VAL', 0.14],
129: ['ARG', 0.12],
130: ['TYR', 0.07],
131: ['ASN', 0.04],
132: ['ASN', 0.02],
133: ['GLY', 0.05],
134: ['GLN', 0.03],
135: ['SER', 0.04],
136: ['PHE', 0.0],
137: ['GLN', 0.04],
138: ['PRO', 0.08],
139: ['ASN', 0.07],
140: ['CYS', 0.07],
141: ['LYS', 0.07],
142: ['TYR', 0.06],
143: ['ASN', 0.0],
144: ['CYS', 0.0],
145: ['THR', 0.06],
146: ['CYS', 0.0],
147: ['ILE', 0.1],
148: ['ASP', 0.0],
149: ['GLY', 0.0],
150: ['ALA', 0.06],
151: ['VAL', 0.16],
152: ['GLY', 0.06],
153: ['CYS', 0.08],
154: ['THR', 0.04],
155: ['PRO', 0.03],
156: ['LEU', 0.08],
157: ['CYS', 0.0],
158: ['LEU', 0.0],
159: ['ARG', 0.04],
160: ['VAL', 0.0],
161: ['ARG', 0.04],
162: ['PRO', 0.06],
163: ['PRO', 0.06],
164: ['ARG', 0.04],
165: ['LEU', 0.05],
166: ['TRP', 0.06],
167: ['CYS', 0.05],
168: ['PRO', 0.06],
169: ['HIS', 0.05],
170: ['PRO', 0.05],
171: ['ARG', 0.05],
172: ['ARG', 0.05],
173: ['VAL', 0.04],
174: ['SER', 0.07],
175: ['ILE', 0.04],
176: ['PRO', 0.05],
177: ['GLY', 0.0],
178: ['HIS', 0.11],
179: ['CYS', 0.08],
180: ['CYS', 0.1],
181: ['GLU', 0.11],
182: ['GLN', 0.07],
183: ['TRP', 0.13],
184: ['VAL', 0.13],
185: ['CYS', 0.06],
186: ['GLU', 0.05],
187: ['ASP', 0.08],
188: ['ASP', 0.06],
189: ['ALA', 0.09],
190: ['LYS', 0.04],
191: ['ARG', 0.02],
192: ['PRO', 0.05],
193: ['ARG', 0.04],
194: ['LYS', 0.06],
195: ['THR', 0.04],
196: ['ALA', 0.12],
197: ['PRO', 0.1],
198: ['ARG', 0.09],
199: ['ASP', 0.0],
200: ['THR', 0.09],
201: ['GLY', 0.11],
202: ['ALA', 0.12],
203: ['PHE', 0.21],
204: ['ASP', 0.12],
205: ['ALA', 0.13],
206: ['VAL', 0.1],
207: ['GLY', 0.04],
208: ['GLU', 0.04],
209: ['VAL', 0.06],
210: ['GLU', 0.04],
211: ['ALA', 0.07],
212: ['TRP', 0.12],
213: ['HIS', 0.08],
214: ['ARG', 0.07],
215: ['ASN', 0.03],
216: ['CYS', 0.03],
217: ['ILE', 0.11],
218: ['ALA', 0.07],
219: ['TYR', 0.08],
220: ['THR', 0.11],
221: ['SER', 0.07],
222: ['PRO', 0.08],
223: ['TRP', 0.19],
224: ['SER', 0.17],
225: ['PRO', 0.2],
226: ['CYS', 0.1],
227: ['SER', 0.26],
228: ['THR', 0.21],
229: ['SER', 0.18],
230: ['CYS', 0.25],
231: ['GLY', 0.26],
232: ['LEU', 0.17],
233: ['GLY', 0.23],
234: ['VAL', 0.16],
235: ['SER', 0.16],
236: ['THR', 0.14],
237: ['ARG', 0.15],
238: ['ILE', 0.16],
239: ['SER', 0.09],
240: ['ASN', 0.06],
241: ['VAL', 0.04],
242: ['ASN', 0.04],
243: ['ALA', 0.05],
244: ['GLN', 0.05],
245: ['CYS', 0.05],
246: ['TRP', 0.04],
247: ['PRO', 0.04],
248: ['GLU', 0.04],
249: ['GLN', 0.09],
250: ['GLU', 0.15],
251: ['SER', 0.11],
252: ['ARG', 0.09],
253: ['LEU', 0.17],
254: ['CYS', 0.12],
255: ['ASN', 0.21],
256: ['LEU', 0.2],
257: ['ARG', 0.15],
258: ['PRO', 0.14],
259: ['CYS', 0.24],
260: ['ASP', 0.15],
261: ['VAL', 0.13],
262: ['ASP', 0.1],
263: ['ILE', 0.07],
264: ['HIS', 0.04],
265: ['THR', 0.06],
266: ['LEU', 0.05],
267: ['ILE', 0.07],
268: ['LYS', 0.08],
269: ['ALA', 0.0],
270: ['GLY', 0.0],
271: ['LYS', 0.0],
272: ['LYS', 0.07],
273: ['CYS', 0.06],
274: ['LEU', 0.07],
275: ['ALA', 0.0],
276: ['VAL', 0.07],
277: ['TYR', 0.0],
278: ['GLN', 0.02],
279: ['PRO', 0.04],
280: ['GLU', 0.05],
281: ['ALA', 0.04],
282: ['SER', 0.04],
283: ['MET', 0.05],
284: ['ASN', 0.05],
285: ['PHE', 0.08],
286: ['THR', 0.04],
287: ['LEU', 0.06],
288: ['ALA', 0.06],
289: ['GLY', 0.0],
290: ['CYS', 0.0],
291: ['ILE', 0.05],
292: ['SER', 0.05],
293: ['THR', 0.05],
294: ['ARG', 0.06],
295: ['SER', 0.06],
296: ['TYR', 0.05],
297: ['GLN', 0.06],
298: ['PRO', 0.06],
299: ['LYS', 0.04],
300: ['TYR', 0.05],
301: ['CYS', 0.04],
302: ['GLY', 0.06],
303: ['VAL', 0.09],
304: ['CYS', 0.07],
305: ['MET', 0.07],
306: ['ASP', 0.06],
307: ['ASN', 0.0],
308: ['ARG', 0.08],
309: ['CYS', 0.0],
310: ['CYS', 0.0],
311: ['ILE', 0.07],
312: ['PRO', 0.08],
313: ['TYR', 0.06],
314: ['LYS', 0.06],
315: ['SER', 0.06],
316: ['LYS', 0.04],
317: ['THR', 0.04],
318: ['ILE', 0.06],
319: ['ASP', 0.0],
320: ['VAL', 0.0],
321: ['SER', 0.04],
322: ['PHE', 0.1],
323: ['GLN', 0.06],
324: ['CYS', 0.0],
325: ['PRO', 0.0],
326: ['ASP', 0.11],
327: ['GLY', 0.08],
328: ['LEU', 0.04],
329: ['GLY', 0.13],
330: ['PHE', 0.16],
331: ['SER', 0.15],
332: ['ARG', 0.14],
333: ['GLN', 0.24],
334: ['VAL', 0.3],
335: ['LEU', 0.3],
336: ['TRP', 0.34],
337: ['ILE', 0.46],
338: ['ASN', 0.55],
339: ['ALA', 0.6],
340: ['CYS', 0.77],
341: ['PHE', 0.71],
342: ['CYS', 0.78],
343: ['ASN', 0.73],
344: ['LEU', 0.77],
345: ['SER', 0.66],
346: ['CYS', 0.72],
347: ['ARG', 0.53],
348: ['ASN', 0.63],
349: ['PRO', 0.5],
350: ['ASN', 0.53],
351: ['ASP', 0.39],
352: ['ILE', 0.57],
353: ['PHE', 0.47],
354: ['ALA', 0.46],
355: ['ASP', 0.45],
356: ['LEU', 0.47],
357: ['GLU', 0.43],
358: ['SER', 0.44],
359: ['TYR', 0.51],
360: ['PRO', 0.4],
361: ['ASP', 0.45],
362: ['PHE', 0.41],
363: ['SER', 0.39],
364: ['GLU', 0.37],
365: ['ILE', 0.33],
366: ['ALA', 0.34],
367: ['ASN', 0.19]}
#for meta-PPISP output, the default positive rediction or whether the residues are at the protein-protein interaction site corresponds to a B-factor score > 0.34
#filter the dictionary to show only residues with B-factors greater than 0.34
#filtered_prediction is a global variable
filtered_prediction = {key:value for (key, value) in prediction_dict.items() if value[1] >= 0.34}
#code check
filtered_prediction
{336: ['TRP', 0.34],
337: ['ILE', 0.46],
338: ['ASN', 0.55],
339: ['ALA', 0.6],
340: ['CYS', 0.77],
341: ['PHE', 0.71],
342: ['CYS', 0.78],
343: ['ASN', 0.73],
344: ['LEU', 0.77],
345: ['SER', 0.66],
346: ['CYS', 0.72],
347: ['ARG', 0.53],
348: ['ASN', 0.63],
349: ['PRO', 0.5],
350: ['ASN', 0.53],
351: ['ASP', 0.39],
352: ['ILE', 0.57],
353: ['PHE', 0.47],
354: ['ALA', 0.46],
355: ['ASP', 0.45],
356: ['LEU', 0.47],
357: ['GLU', 0.43],
358: ['SER', 0.44],
359: ['TYR', 0.51],
360: ['PRO', 0.4],
361: ['ASP', 0.45],
362: ['PHE', 0.41],
363: ['SER', 0.39],
364: ['GLU', 0.37],
366: ['ALA', 0.34]}
#print the filtered prediction output without the B-factor scores to better visualize the data
for k, v in filtered_prediction.items():
print(k, v[0])
336 TRP 337 ILE 338 ASN 339 ALA 340 CYS 341 PHE 342 CYS 343 ASN 344 LEU 345 SER 346 CYS 347 ARG 348 ASN 349 PRO 350 ASN 351 ASP 352 ILE 353 PHE 354 ALA 355 ASP 356 LEU 357 GLU 358 SER 359 TYR 360 PRO 361 ASP 362 PHE 363 SER 364 GLU 366 ALA
The residues of interests based on the data analysis above is colored in violet.
HawkDock Server and PyMOL
For protein-protein interaction analysis between the constructed WISP-1 model and specific proteins, the web server HawkDock (http://cadd.zju.edu.cn/hawkdock/) might be able to give more insights. You can submit to the server the WISP-1 model file and the PDB file of an interacting protein of interest. The protein of interests investigated for this project is β-catenin, which was identified as a binding partner of WISP1.
Submit the WISP-1 model constructed and the PDB structure file of β-catenin (PDB ID: 3SL9) to the server. You can put either one as ligand or receptor. The result should arrive within 72 hours and can be retrieved from a URL sent to you if you leave an email when submitting the job to the server.
Here is the result page that the URL should direct you to:
Click download top 10 predictions. We will be analyzing model 1 from the top 10 prediction.
Display within PyMOL the model.1.pdb file you just downloaded from the HawkDock Server. Click S at the bottom right bar to display the sequences of the polypeptide chains of both WISP-1 and β-catenin. Select each structure and put them in different color by selecting C on the right to modify the color they are displayed in. WISP-1 is in orange and β-catenin is in cyan.
Since we want to find out what residues on WISP-1 is interacting with other proteins, click H on the WISP-1 selection to hide all of the WISP-1 structure. Now type into the top bar the following code: show sticks, byres all within 5 of _( insert in the blank the name you set your β-catenin selection to).
For example, my code reads: show sticks, byres all within 5 of beta-catenin.
This code will show all the residues in sticks within WISP-1 that are within the distance of 5 angstrom from β-catenin will be shown.
code source: https://pymolwiki.org/index.php/Selection_Algebra
Zooming in, it can be observed that 359Y, 360P, 361D, 362F, 363S, 364E, 366A, and 367N are predicted to be WISP-1 residues that are within proximity of β-catenin and might be engaging in interaction. 367N of this model specifically is likely to be engaging in hydrogen bonds with β-catenin residues 40K and 42E (indicated by yellow dashed line)
To find the hydrogen bonding, select WISP-1 selection —> A —> Find —> polar contact —> any other atom. Yellow dashed lines will be used to display hydrogen bonds.
The same analysis was performed for model 2 from the top 10 predictions.
357E, 358S, 359Y, 360P, 361D, 362F, 363S, 364E, 366A, and 367N are predicted to be WISP-1 residues that are within proximity of β-catenin and might be engaging in interaction.
364E and 367N of this model specifically is likely to be engaging in hydrogen bonds with β-catenin residues 603K, 605E, and 607Y.
The protein structure for the WISP-1 (CCN4) protein, which currently has no existing experimental structure stored in the PDB, was generated using homology modeling with existing template 5nb8 which has a 53.52% sequence identity and an e-value of 2.45677e-19. 5nb8 is a structure of vWC domain from CCN3, another member from the CCN protein family. Using a Ramachandran plot, the model was evaluated to have 81.9% of residues are in the most favoured regions, 13.2% residues are in the additional allowed regions, 3.5% residues are in the generously allowed regions, with only 1.3% of residues being in the disallowed regions. Now we would proceed to do interaction analysis using this model we generated. Given that the most closely related template structure available in the PDB has a sequence identity of 53.52%, although 81.9% differ from the 90% residues usually expected to be in the core of favored region of the protein for a good protein structure (1), the model we generated could be a reliable start point for further prediction evaluation.
Then the WISP-1 structure is analyzed via different structure-based online server for protein and protein interaction. For a general analysis, it was found that the amino acids ranges from 336W to 366A, exlcuding 365I and 367N are predicted to be likely residues at the protein interaction interface. For a more specific analysis with β-catenin structure (PDB ID: 3SL9), a series of interaction prediction is generated with different structural models for specific site interactions. Model 1 and model 2 from the top 10 predictions were used for analysis. In model 1, WISP-1 residues 359Y, 360P, 361D, 362F, 363S, 364E, 366A, and 367N are predicted to be within proximity of β-catenin and might be engaging in interaction. Model 2 has prediction of 357E, 358S, 359Y, 360P, 361D, 362F, 363S, 364E, 366A, and 367N being WISP-1 residues interacting with β-catenin. This matches the general prediction analysis in that the residues from 336W to 366A might be involved at an interaction interface with another protein. The model also predicted specific hydrogen bonds between WISP-1 and β-catenin. Intermolecular hydrogen bonds being present demonstrates the binding complexes are reliable, given that hydrogen bonds are known to stabilize protein-ligand complexes (2) and that the docking results are significant (3). With the homology modeling structure helping to elucidate residues potentially involved in molecular docking between WISP-1 and its binding partner β-catenin which together they mediate tumor formation and progression, this might provide insights to what might consitute suitable inhibitors to adequately block their specific interactions to slow or prevent tumorgenesis.
Sources cite:
local variable: variables defined inside a function and its scope is limited to the function only.
source: https://www.geeksforgeeks.org/global-local-variables-python/